I've had several subs and have quite a bit of experience with integrating them. There is definitely something to the claim that having multiple sets of interconnects can mess up the sound. It isn't always a problem but I've found that my benchmark dacs can't drive both the amplifier and a sub. The bass quality is surprisingly degraded. On the other hand, my Bryston pre can drive both amp and sub with no problem with no noticeable change in quality.
I hate to say it but after having my systems in 5 different houses the best way to integrate a sub is to have your system in a large room in a house that has fairly lightweight construction. I've had my system in multiple basements, smallish rooms in brick houses, medium rooms in frame houses, smallish plaster rooms in frame houses, and now in large rooms in a frame house. I've also bought digital equalizers, made over 2 dozen bass traps and gone through extensive measurements with a measurement mic, real-time analyzer and various tone generators and discs.
If I were you I'd buy the behringer ultra-curve and measurement mic (or something similar). Get a tone generator. This will let you do a direct comparison of the signal being fed to the system vs the actual volume that is present at the microphone. If you do this it will give you a sense of proportion that I don't think you'll get any other way. If you have a 12db peak at 60hz and a 12db null at 45 this will let you hear it and know what you're hearing. You'll be able to completely squash the peak, although you'll probably be a little surprised at how deep of a cut you have to make to actually get rid of the bloat.
Once you quantify what you're hearing you will be able to decide what you want to do about it. You can make huge cuts to completely get rid of the peaks but in my opinion this won't sound right. It seems to kill transients. You can make a bunch of bass traps and that can help with the peaks without doing as much harm as huge eq cuts but it's either very expensive or a lot of work to get enough of them to really make a big difference. In my experience it's impossible to completely fix a bad room, although the problems can definitely be reduced. I haven't tried the processors that do processing in the time domain as well as frequency and I haven't tried making any sort of resonator. I'd like to try it someday just to see how it works. Sadly, I've got systems in really good rooms now and I don't have troublesome resonances that are bothering me.
I hate to say it but after having my systems in 5 different houses the best way to integrate a sub is to have your system in a large room in a house that has fairly lightweight construction. I've had my system in multiple basements, smallish rooms in brick houses, medium rooms in frame houses, smallish plaster rooms in frame houses, and now in large rooms in a frame house. I've also bought digital equalizers, made over 2 dozen bass traps and gone through extensive measurements with a measurement mic, real-time analyzer and various tone generators and discs.
If I were you I'd buy the behringer ultra-curve and measurement mic (or something similar). Get a tone generator. This will let you do a direct comparison of the signal being fed to the system vs the actual volume that is present at the microphone. If you do this it will give you a sense of proportion that I don't think you'll get any other way. If you have a 12db peak at 60hz and a 12db null at 45 this will let you hear it and know what you're hearing. You'll be able to completely squash the peak, although you'll probably be a little surprised at how deep of a cut you have to make to actually get rid of the bloat.
Once you quantify what you're hearing you will be able to decide what you want to do about it. You can make huge cuts to completely get rid of the peaks but in my opinion this won't sound right. It seems to kill transients. You can make a bunch of bass traps and that can help with the peaks without doing as much harm as huge eq cuts but it's either very expensive or a lot of work to get enough of them to really make a big difference. In my experience it's impossible to completely fix a bad room, although the problems can definitely be reduced. I haven't tried the processors that do processing in the time domain as well as frequency and I haven't tried making any sort of resonator. I'd like to try it someday just to see how it works. Sadly, I've got systems in really good rooms now and I don't have troublesome resonances that are bothering me.