Here is a link to the FAQ section of the Audyssey website:Audyssey FAQ
This Q/A is of particular interest:
What happens to the MultEQ settings when the parameters are changed? MultEQ corrects for room acoustical problems. Changes in the tone controls do not change the filter performance. They do change the tonal balance based on the preferences of the customer. The benefit of MultEQ is that it allows a customer (or installer) tone control setting to work on all program material in a much more predictable way than it would on an uncalibrated system. Changes made to the crossover frequency or small and large settings of the loudspeakers will affect the performance of the MultEQ filters and Audyssey does not recommend changing them.
I've been playing around with the speaker settings because after a dozen calibration routines, Audyssey still sees my center speaker as Large, which it is certainly not. It's interesting: when I change the center speaker to Small, the cutoff frequency is automatically set to 40Hz. That's OK, and if I make just that one change, I still have the impressive sound-stage that Audyssey produces. It seems that any other changes to speaker level or changing the cutoff to 80Hz will negatively impact the sound-stage. Therefore, there seems to be very little flexibility in tweaking an Audyssey calibration.