Yes, the 3808 has independent crossovers. My suggestion would be to run the Audyssey and see how it sounds then make adjustments from there.
I have the 3808 and I adjusted the Audyssey settings to this, my M80s at 40, VP150 at 60 and QS8s at 80 and I really like it. Then again I have a poor sub so that could be why I need more output from my speakers. The program set them to M80s at 40, VP150 at 60 and QS8s at 60 too. I have a poor sub so this could be why I need more output from the speakers than most.
It took me awhile to get used the settings (EQ and freq.). After awhile I started to notice I could hear some things better than before but some other sounds lost a little as the Eq did its job.