The 990 will make an attempt to set up your crossovers, but there's nothing sacred about what the auto-setup comes up with. In your case, I suspect that the crossovers were set a bit too high and the auto-setup made a few less than ideal decisions. Fortunately, you can adjust the bass management settings and the only other setting you may want to adjust would be the sub's trim (which is one that many people end up fine-tuning by ear anyway). I'd suggest setting all of your speakers to small and use a 60Hz crossover for the mains. The center and bookshelves will probably be best with an 80Hz crossover.

If you want to run your mains full range for two-channel listening, the easiest way to do that is to set them to "large." Bass reinforcement using the sub could be achieved by setting the sub to "L/R+Sub," which will use the mains' crossover point to produce a signal for the sub while leaving the mains' signals full range. An alternative that would work if you listen to CD's in a player with really good DAC's is to use would be to use the player's stereo analog output and the 990's bypass mode, which would also send a copy of the left and right channels to the sub - but with your current system, this isn't really an optimal approach since the best DAC's in your system look to be the ones in the 990. I'd actually suggest experimenting with three things: mains large with 60Hz crossover and sub "l/r+sub;" mains large and sub "lfe only" (crossover of mains not used); and mains small with either 40Hz or 60Hz crossover. If the sub feels a bit excessive in any of these cases, there's an option in Surround Config called 2-Ch Sub Offset that will let you basically turn the sub down a few dB when in a stereo mode.