Subwoofers masking other frequencies.

Bought a third sub,a svs sb2000 to add to my existing 2 subs hoping for stronger and more detailed bass response. My mains are magnapan 1.7i driven by parasound A21 +. After messing around with  different ways to intergrate the subs I realized some parts of the music was missing or reduced in volume or one channel was stronger .well I turned off one sub at a time and the sound was full. Is this common and what's the remedy for this phenomenon. 

Sounds like destructive interference. You'll need to adjust delay/phase/position to ensure the sound from all the subs and your main speakers arrive at your seating position at the same time. Room EQ Wizard can help by measuring each speaker and subwoofer individually, relative to each other (see for an example).
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My initial guess is that it's an integration issue, and that the subs are contributing too much energy a bit north of the subwoofer region.  

Make sure you aren't using the LFE inputs, unless you are using a home theater processor.  And even then, you might want the additional roll-off of using the normal music inputs.  

I suggest reducing the lowpass filter frequency on all of your subs to the minimum, which looks like 50 Hz for the SVS B2000.  That may still be on the high side, given that the lowpass filter slope is only 12 dB per octave.   

Then adjust the level control, which will make a big difference, and then the phase control, which will probably make a small difference.   Cycle back through fine-tuning a few times.  The level control may take a long time to dial in, as very small changes in sound pressure level make  disproportionately large changes in perceived loudness at very low frequencies.   

You can go back and try raising the lowpass filter frequency after you've gotten the level and phase dialed in, but if all three of your subs are the same SVS model then the 50 Hz minimum might end up being your best bet.   


What should I expect from the adjustable phase knob. Vol. Increase ? Smoothing of tone?
Thanks for the help.
 The phase knob mostly affects the blend between subs and mains.  When it SOUNDS right, it IS right.  There are too many variables to predict in advance what the "right" setting will be, but in the end what matters is how it sounds.  Don't be afraid to make big adjustments.   

I took your advice and set the crossovers to dead bottom and slowly increased volume  winsome good results. 
Thanks for your help Duke
Yes, Audyssey will help you, but it is still a starting point. I don’t think it does much in the time domain. You will need to raise the level a couple of dBs from what Audyssey recommends for it to sound realistic. Good luck. 
This is about the phase control you know you’re in phase when all your speakers are moving in and out exactly at the same time.To do this you simply move the phase knob from 0 to 180 until You achieve the loudest sound then you are in phase. Hope this helps.Best of luck
While it's true that you'll get the loudest sound in the crossover region when the sub is "in phase" with the main speakers, that may not be what sounds best.  IF one of the issues is too much contribution from the sub in and above the crossover region, then partial cancellation may actually sound better, which is why I said that "when it sounds right it IS right".   

Audiomaze - what are your existing two subs?   Also, are you using an SB-2000 or the newer SB-2000 Pro?
Audiokinesis While It’s true when it’s right it’s right. I believe once you get your speakers in phase then you need to readjust the gain on your sub and perhaps change the crossover point.I wouldn’t want my speakers out of phase. Just trying to help Duke not trying to argue.Warmest Regards
My existing two subs are Klipsch rsw10 and Sony 8"both are ported. I have  the SVS and the klipsch hooked up and sounding pretty good. 
Needfreestuff, I understand and appreciate that your intention is to help, not to argue.  So is mine!  And in an ideal situation I'd agree with you that it makes sense to have mains and subs in-phase in the crossover region.  

In audiomaze's situation, wherein it sounds like the issue may be too much energy contributed by the subwoofers too high up the spectrum, and where the minimum lowpass filter frequency setting (50 Hz) is not all that low, imo a bit of destructive interference can make a positive contribution.  

Another such situation is where the mains have an intentionally exaggerated upper bass response to compensate for a lack of actual low bass response.  This is sometimes the case with mini-monitors.  Once again, a bit of destructive interference can cancel out that upper-bass emphasis.   

A third such situation is where we're trying to squeeze a little bit more low bass out of our sub(s).  If we don't have EQ available and can't reduce the lowpass filter frequency any further, sometimes we can use a bit of destructive interference to reduce the top end of the sub(s).  So instead of raising the bottom end of the sub(s), we're reducing the top end.  Then we can increase the level a little bit to make up for the destructive interference with the bottom end of the mains, and in effect we have raised the bottom end of the subs relative to the rest of the spectrum.  

There is even a small theoretical advantage to overlapping with the mains a bit and dialing in some phase differential to smooth the response in that region:  We now have more in-room sources spread around the room in the overlap region, and the net result is likely to be a bit smoother in-room response over a wider range of listening positions.  

And since the ear's time-domain resolution is poor in the subwoofer region, there is unlikely to be a downside to the subs not being perfectly in-phase with the mains through the crossover region, as long as the net frequency response is good.  In the bass region, speakers + room = a "minimum phase system", such that the frequency response and time-domain response track one another.  When we have fixed one, we have simultaneously fixed the other.  

sounds like adding the third sub created the condition. 
as others have mentioned most likely too much energy in the room at frequencies shared by the main speaker.  
1) first off- how do you have them connected?  if two subs are connected to the same channel that might draw enough current to make the main speaker of that channel have reduced volume compared to the other.  
2) what are the makes and model of your other two subs?  
3) the SVS may also have cabinet resonance in the audible range that (unfortunately) the crossover frequency cannot control.  

The two subs are hooked to a parasound p5 pre thru two sub outputs we low pass options  which are switchable to direct full bandwidth output.