Okay, I went from a Denon 3805 to the 990/7700 combo and when I first hooked it up something didn't seem to sound right. I tried setting the front speakers to large but something still just didn't sound right. After messing around with the settings I set all speakers to SMALL, X-over set at 80Hz. on all speakers and set the subwoofer to YES. Once that was done I ran the auto calibration feature and with some fine tuning everything played just the same but better than the 3805.

My suggestion would be to do exactly what I did and see what happens. If you haven't already, disable the crossover on the subwoofer itself and let the 990 do the work. If you unable to disable the x-over on the subwoofer, set it to the maximum setting that way you don't have to worry able double filtering.