Shouldn't an off the shelf, powered, ported sub like his have a HPF built in to avoid over-excursion below the tuning frequency? It sounds to me like this is a simple case of the subwoofer feet sinking too far into the carpet. Get them back up above the carpet, and go on your merry way.
I do agree though that you should probably raise the crossover frequencies from where your receiver set them. Otherwise there's nothing else you should need to change. Audyssey should have handled the phase setting of your subwoofer, so it should be fine wherever it was. The gain knob on the subwoofer can be anywhere, as long as you don't mess with it after running audyssey. The only potential issue is if audyssey maxes out the level adjustment for the subwoofer. If it shows you that it set a level between -5 and +5, it's fine.