Most recommendations I've seen on A.V.S. regarding Audyssey say set after running so as to let the subs Amp.s do the heavy Bass. As they're designed to.

We with Anthems A.R.C. Genesis have a thread on there. It likes to set all speakers to +12 and subs to 2 or 3. Regardless of external amplification. The sound is still Phenomenal, though most worry it's to high.