Ok I have pondered this for a little bit but Lets say you have the gain on the amp set at X, with the remote knob at full tilt, does the amplifier run at full tilt? or will it stop at "X"?
The remote knob that increases your bass? Isn't that for your bass boost on your amp? So if your gain is set to X and you use the knob to increase your bass, you'll be increasing the voltage and can cause your subs to get a clipped signal.
If you want to use the bass remote, set your gain with the bass remote at the max.