I just wanted to highlight some of the stuff a few of us have caught crap for saying here before.
Also (and I've said it before here many times) Audyssey and other auto-setup/EQ systems are error-prone so don't rely on their settings as absolute. If your ears tell you otherwise, then play with the crossover settings and the Small/Large settings. It varies so much with room size and with speaker location.
In my particular setup (an average room size of 2,100 cu. ft), if I set my M80s to "Large" and use my EP500 subwoofer, I get way too much upper bass. The best balance is with the M80s set to Small and an 80-Hz crossover (which I use for the center and the surrounds). Ian at Axiom, in his big cathedral ceiling living room uses 40 Hz on the M80s.
As a default setting to start out with, it's hard to beat an 80-Hz crossover and Small settings for all the speakers. It's why I recommend it, and also why Tom Holman of THX recommends it. Then if you want play with Audyssey or some proprietary auto-setup system, go ahead and use the one that sounds best to your ears in your setup. It's just that we get complaints at Axiom of "not enough bass" or the like and when I or the audio experts investigate, we find the customer has used Audyssey or another auto-setup that has clearly miscalculated on the crossover frequencies, subwoofer setup, and speaker size settings.
