A little confused on how to properly integrate my sub

unfortunately you are going in the wrong direction if you want seamless integration between sub and the LS50s (which is completely possible!).  
the issue is your subwoofer- it lacks the necessary adjustments needed for proper integration.  critical controls like a polarity switch and continuous phase angle adjustment.  
REL used to offer these controls- it is a shame yours does not have them.  
rather than getting the outlaw amp (sending your LS50s through more electronics is not optimal) i would suggest a sub like the JL audio D110, which has the proper controls for perfect integration.  
If you use the foam plugs on the LS50s, they will have an acoustic crossover frequency of ~ 75 Hz- where the bass drops like a rock.  set your crossover on the sub to ~ 75Hz.  your default setting for the subwoofer should be reverse polarity (helps avoid peaks and valleys) and then rotate the phase control until the sound is seamless.  
if you get a sub with the proper features you can keep your current amp.  getting a new amp with sub crossover is a losing battle without the right sub.  unless you aren't particular - but you already are because you want to make a change.  change the sub, not the amp.  

You are correct that you don’t want to run your speakers through the sub if you can avoid it.  Hook the LS50s directly to the RR2160 and the sub directly to the RR2160 via the LFE or RCA low level input, set the crossover on the sub to its highest value, and then use the crossover dials on the RR2160 to set the actual crossover point you want.  

@avanti1960 is right in that the REL doesn’t seem to have a phase or polarity switch.  That may or may not be an issue depending on where it’s placed and your room.  Try it out and see how it works first.  

Another option would be to get an integrated amp with the smarts to automatically adjust phase and polarity.  The Yamaha R-N803 or the Elac Element EA101EQ would both be great choices, and both cost around the same as the RR2160.  They both also have room correction built in to even better improve your sound. 

@avanti1960 Thanks for the recommendation. I mostly got this sub because it was a ridiculously good deal and didnt put a whole lot of thought into how it would fit into my system. For the time being, is going from the outlaw crossed over at 80hz into the LFE input a decently acceptable option? I know going into the low level input is going to take me through another crossover. I figure that the LFE input probably has less in the signal path and isnt going through some sort of filter since its a standard. 

Tithe -3 dB point for the LS 50 is 79hz.  Just let them roll off naturally and use the REL as the manufacturer intended.  You’re headed in the wrong direction.

+1 with rhljazz, good rec.

Yeah letting them roll off naturally will sound great if you don’t want to play them very loud. If you play music with any bass to those little drivers at full range don’t expect too much volume. Been there done that. 

Get an SPL meter (even if a free one on your phone), use C weighting. Load up an online tone generator, measure how loud the LS50 is from say 500Hz-5000Hz, and get an average SPL level for that region. Then, lower the frequency until is drops 6dB from that average you found. Then, set the crossover  on the Outlaw on the sub and speakers at that frequency (maybe play it say and have a slightly lower crossover for the speakers, like if you found it to be 50Hz, set the sub crossover to 50Hz and maybe the speaker to 40Hz).  
  
Now, I assumed you did the sub crawl. Next, is phase (or in your case, cause REL are jackasses, a polarity switch). Whatever crossover the subwoofer is set to, load up that same tone generator website and play the crossover frequency tone (50Hz from the previous scenario), then flip the polarity switch until it sounds louder (use an SPL meter or have someone help, one person sits down in the seat and the other flips the switch), The louder setting is the correct one, as that means they are in-phase (if out of phase, they would negatively interact, decreasing output; in-phase interacting at -6dB leads to 0dB sum, so flat).  

Mans yes, use the LFE jack.

You have a philosophical choice here:

The "audiophile" way is to play the Kef full range and integrate the Rel as Rel suggests. This is hands-off and maintains the simplest signal path.

The "rationalist" view is to actively cross. This will dramatically reduce distortion. The LS50 (like all speakers using smallish mid bass cones to cover LF) will show dramatically increasing distortion as frequency drops and spl increases. That’s physics. Actively relieving the Kef driver of duty below 100 hz will clean up low end distortion very effectively.

The question is whether it matters. Some say that the ear is insensitive to THD at low frequencies. You have to decide.

BTW - If you do decide to actively cross the system, I’d seriously think about an amp with a digital x-over and room EQ (per the earlier suggestion). It appears that you use exclusively digital source material and IMO crossing in the digital domain is the way to go. IME room correction is the single biggest improvement I’ve ever made to a high end set-up, but you can always defeat it if you prefer that route. (You won’t)

BTW - If you do decide to actively cross the system, I’d seriously think about an amp with a digital x-over and room EQ (per the earlier suggestion). It appears that you use exclusively digital source material and IMO crossing in the digital domain is the way to go. IME room correction is the single biggest improvement I’ve ever made to a high end set-up, but you can always defeat it if you prefer that route. (You won’t)

Thanks! I know that the Outlaw utilities an analog filter. I have some AVRs sitting around but I know those probably don't play well with the KEFs due to impedance. Do you have any recommendations for amps with a built in digital crossover? As far as room correction goes, Im sure it would be nice but Im using these near field on ISO Acoustics stands at my desktop computer so im not sure how effective it would actually be.

I mentioned it above, but the Elac Element EA101EQ is a great choice for a desktop integrated, I use one myself with a pair of Elac Uni-Fi UB5s and an SVS SB12-NSD for my computer audio.  It has digital and analog inputs, an asynchronous USB DAC, and an auto-blend function to automatically match your bookshelves to your subwoofer.   It's fine with 4ohm loads so the impedance swings of the LS50s won't bother it.

If you’re concerned about the amp section of an AVR, go for a modest Pre-pro and a stereo power amp of your choice/budget.

IIRC, NAD makes a higher end integrated with these features that’s pretty costly. DEQX and Lyngdorf make excellent products, but they’re even more expensive   The Elac recommendation above is probably the most cost effective solution that I’ve seen.

Okay, I didn't read all of the responses and someone may have caught this already. First, I personally think you're going the wrong way by selling the MF integrated in favor of the Outlaw. Especially considering how REL subs are intended to integrate. If you were to keep the MF, you would connect the sub's high-level (Speakon) jack to the speaker jacks on the amp. Leave the black wire hanging unless you get hum. If you do, ground the black wire to the chassis. You'd start near 12 o'clock with the x-over and volume on the sub and the phase at 0 deg. First, flip the phase switch on the sub back and forth until you figure out which setting produces more bass. Leave it that way. In my experience it's 0 degrees more often. Then adjust your crossover and volume settings until the sub blends smoothly with the speakers. You shouldn't really hear the sub per se, it should just extend the low end response of the speakers and improve sound staging etc. FYI, REL suggests their subs be placed in a corner if possible. The boundary reinforcement helps with extreme low frequencies but sub woofer placement is an important part of correct integration. You'll need to move and aim the sub so it sounds best and this will take some experimentation too. In my experience, even small adjustments make audible differences. Same with the speakers. The other thing I've noticed with REL subs is that they seem to me to like some break-in time and when they've been properly broken in they integrate more seamlessly. So do your best and don't be afraid to make minor adjustments over time.

A note on the difference between some of the other subs suggested compared to REL... Most sub woofers have significant group delay/impulse response time delay as a result of the amplifier and signal processing necessary to get small boxes to make big bass with extension down in to the mid-20HZ range or lower. This is not insignificant. JL Audio themselves will tell you that their subs have around 15 milliseconds of delay. This may not sound like a big deal, but it is. 1 millisecond is equal to about 1 foot so if a sub introduces 15 milliseconds of delay it's like placing your sub woofer 15 feet behind your speakers. REL handles design of amplifications differently and while their subs still introduce some delay, it's less significant. This is why the high-level connection works.
So if you do go with the Outlaw and you want to cross over and use the bass management, you can. Thought this is not recommended by REL. You WOULD use the .1/LFE input because it does not have a crossover in line. It's intended for connection to the LFE output on a AVR when used as a home theater sub and will work equally well in your application. If you do go this route, I would begin your setting up with the sub/speaker crossover point around 60 HZ and work from there. If the Outlaw has bass management in depth enough to include the ability to compensate for delay, with the REL I'd probably start with around 5-7' of delay and see how it works. You can always go up or down from there.

There has been a ton of pub in the last few years as audiophiles continue to embrace sub woofers as a viable part of a listening system. A lot of the pub is incomplete in my opinion. I think JL and many other manufacturers make good products but I don't think it's possible the achieve the level of seamless integration with them as you can with REL unless you have a way to time-align them at the crossover frequency. This requires DSP. Just adjusting phase on the sub does not do this. You cannot compensate for delay by adjusting phase on something that starts life 15 milliseconds behind your speakers. You must be able to delay your speakers so that they align with the sub. Many audiophiles are purists and adding DSP is sacrilege. For these people, in my opinion REL, or similar designs are the only way.

I've heard many REL subs in my years of designing home systems. Set up correctly, I think they are one of the single largest potential improvements in virtually any system and with almost any speaker. I've made JL subs work beautifully as well but with the addition of something like the McIntosh MEN220 which employs Lyngdorf RoomPerfect and the ability to make fine adjustments for delay. The last JL G213 took, if I remember correctly,  close  to 17' of compensation to time align with the Mac driven Sonus Faber main speakers. Being in the profession I have access to almost any product I could possibly want. I own two RELs. A T9i in my AV system and a S/3 in my small 2-channel system.

If your only source is your computer and you want to run "digital crossovers", the best approach is to run the digital xo inside the music software in your pc, then output to a multichannel DAC, and drive the sub/s on 2 channels and the LS50 on other 2 channels.

FWIW I started like this and now do 3-way active xo with a Lynx Hilo (DAC). 

I hadn't ever considered it, but Lewinski's idea strikes me as potentially very cost effective.  If I understand the proposal correctly, you'd only need to add the DAC and a multi channel power amp of your choice.  

However, the one caveat here is volume attenuation.  If it's done in the digital domain, you may find that there's an audible impact on SQ (particularly at lower listening levels).  As with all things audio, this is personal and you might also find that it has no impact on SQ.

If attenuation is controlled by the software, then you're effecting it in the digital domain.   If volume control is at the DAC, it could be in either (depending on the design of the DAC) the digital or analog section, but you'd hope it would be analog - in any event you can check the user's manual to find out.

I've never tried it, so I'm not taking a position one way or the other, just pointing out that - if the volume control is in the software - this is the "rationalist's" trade-off in this otherwise very rational solution.

I think you are going backwards.  The M3si is a perfect match for the LS50s.  The REL sub would seem to be a perfect match as well (using the high level input).  The trick here is moving the sub around until you get optimal room pressurization (I'm not going to get into room acoustics and DSP here, other than to say attention to both can yield remarkable results).  The other "trick" is having realistic expectations.  The LS50s are only going to throw out so much sound.  You could easily dial in too much bass with the sub.  I have a similar set up (Harbeth P3esr speakers. REL t5i).  I have both the crossover and level on the sub set at about 9 o'clock, just enough to add a bit of room pressurization.  Any more and the integration with the Harbeths is gone.

If you are looking for big, thumping bass or home theater type sound effects, you can turn the sub up.  But for most music listening, good integration is going to be a lot more pleasurable.

I also agree the 2160 is a step in the wrong direction......  I had a 2150 and returned it..... not because of the sound, the Balance and Bass molex connectors were swapped during manufacture.  The Balance affected the bass and vice versa....  such a turn off I just sent it back.