I always calibrate using 70db as I feel you get a more precise measurement near the "0" mark of the SPL meter and have the preamp set to -10. After doing so, I usually listen to the unit at about -20 for movies and may approach -15 for music.

I used to have the 2500 myself (used only as a pre/pro) and went to the 990. If the sound is muddy, it is most likely due to your crossovers. It took me quite a while to get it set so the bass was properly integrated with everything. You may want to raise you crossovers on the fronts to 80Hz as this will send more of the lower bass to the sub (you said it was not bassy enough).

I found 60Hz to leave things a little too bright and 100Hz left everything a little too muddy. 80Hz ended up being just right. Don't worry about setting the crossovers higher than what your speakers will go down to (my fronts/center will go down to about 40Hz, but I still cross them over at 80), let your ears be the judge of what sounds best.