Welcome, Jeremy!
Do yourself a favor, and pickup a Radio Shack sound level meter (unless you have one lying around already) and just balance the system's levels manually w/o Audyssey. Try that for a week or two before running Audyssey again so you have a point of comparison.

Some feel that Audyssey helps, some feel it really hurts. I know you can likely bypass it for comparison, but then the speakers aren't balanced, either.

Give yourself two weeks to establish a baseline!

::::::: No disrespect to Axiom, but my favorite woofer is my yellow lab :::::::