Sub users...

Bass frequencies are sent to both channels in 99.9% of mixes. Below around 100 Hz you cannot tell where a sub is anyway (if you can it is because leakage of higher frequencies - you can use a steeper filter in the case of a poor quality distorting sub). Your fear is really unwarrented if you intend to get a high quality subwoofer and correctly match it with your mains.

If you buy a ported boom box of a subwoofer then it will indeed ruin Dave Brubeck but not because drums will jump around but mainly because of masking from all the bass resonance and poor transient response from a cheap sub. The most expensive driver on large mains is usually the big woofer. The hardest and most energy demanding driver on any speaker is the woofer and the LF. Logically you might expect to pay as much (or more) for a subwoofer as your mains in order to maintain a similar level of quality.

Did you consider a Wilson Watch Dog? Your speakers have a Q resonance bump around 80 Hz - you can see this on Soundstage measurement plots. This probably affects group delay also and the way the speaker integrates in the room. (speaker may resonate after the music stops up to an extra cycle or so due to this "tuning")

I have no experience adjusting to this speaker but it may be important to match this resonance to get smooth integration. For example, an SVS PB13 Ultra has three ports which you can block or unblock in order to adjust Q resonance (will affect group delay) and this might allow more seamless integration (you get four options of resonance and group delay by blocking none, 1, 2, or all three ports)

Perceptively, lower group delay will give a tighter bass sound kind of like a traditional Basie jazz drum set (just a hint of kick through room pressure). Higher group delay will give you a fuller rock kick drum sound in the bass.

I have been reading about the JL Audio Fathom F113 and one concern I have is that a couple reviews stated that the F113 lacks a high-pass filter, which can be an issue for two-channel use, unless I use an external x-over, which I do not desire to do.

You can always use the sub to fill in and run the mains full range.

Can you expalin possible negative effects of running the mains full range?

Possible problems are matching the large LF phase swings in your mains (due to the double ported design) and/or too much bass at some frequencies.

FWIW: I use the sub to fill-in because I want to take advantage of the different room placement of the sub to allow it to reduce suckouts at the listening position due to inevitable room rear wall reflections and room modes from a symmetric placement of the full range mains. I think this is the best approach if you have good full range speakers and a sub that matches (the drivers and overdamped tuning in my sub precisely match the mains - differing by only a few hertz at resonance). The only reason to restrict full range speakers with a crossover would be in the case of small satellite speakers with 6 inch woofers that can't really handle the LF.

A sub can easily be EQ'd with a Paremetric Equalizer (or TACT or PARC) so that it "fills-in" leaving a pure unfiltered signal to go to your mains. Some subs come with great auto-EQ features. For other less sophisticated subs you can look up Room EQ Wizard for suggestions.

The essential thing is to get a sub that integrates with your speakers! If your speaker resonates and has a highish group delay then a sub that is overdamped and does not resonate will be a waste of money (huge expense for poor SPL output that is tighter than the bass from your mains and therefore a largely inaudible benefit)

According to this article, [url=http://www.stereophile.com/floorloudspeakers/920/index6.html]the WATT/Puppy 7 offers enigmatic measured performance[/url]. This is why it might be safest to get a Wilson sub that is designed to go with them. This speaker is not designed to easily integrate with a sub, IMHO.

will not be using the subs with W/P's

Oops sorry - if they make a matching sub then I'd recommend that.

In the meantime, I found a good example of what typically happens to phase and group delay in different type designs of bass response. It is worth remembering that when you add a sub to full range mains that you may be trying to integrate responses from two completely different designs (different delays of phase). Note how the phase response really separates below 40 Hz for different tuning.

So depending on the different design between speaker and sub you might be out by as much as 90 degrees or more (quarter wavelength) at 20 Hz and yet in phase at 80 Hz or vice versa.