Jim;
Good question. I am actually using the Audyssey Pro for my 4 subwoofers only. I am still using Audyssey built into my Denon 5805. Its a bit complicated, but the combo of the 2 is quite awesome if you spend the time to tweak, and measure the results.
I am still working on this system as we speak and you will see a few additions shortly as well as an editorial on how I am calibrating the bass using Audyssey.