As you probably already know, Audyssey does a fantastic job of correcting speaker response in the room. In a way, it acts like an equalizer, except without many of the downsides of an EQ. It also corrects time delays, and other things.
Well, when you calibrate your system with Audyssey, it's meant for room modes, assuming your speakers are already close to flat. Well... if you speakers aren't flat, Audyssey still fixes it, within the limits of what it can correct. Try to get it as close as you can, while biasing it a little to the lower end (that's just my experience; yours may be different). Then run the full microphone calibration like you normally would. I think you'll be happy with the results. I know I am. :)
IBJamon