sms-1 with denon3806 and audyssey?

Hello all, I posted a question the other day in audio setup forum but had not gotten a response so I figured it may be better to post it here anyway. I have a SMS-1 and a Denon 3806 and was wondering on the order I should setup things ...I can eq the sms-1 then run the audyssey which I have done but audyssey seems to change either the sub distance the crossovers or both and in turn messes up the frequency response unless I go back and change the phase on the sms-1. Can I change the phase on the sms-1 after I run audyssey auto setup ??? Also when eq'ing the sub on the sms-1 should I unhook the main speakers or no ??

Thanks for the help,
Brian

thanks kal, i read your reply and posted this question there also, i wanted to ask you about the phase adjusting part with the sms-1. After I eq with sms-1 and then run audyssey is it ok to then go back to the sms-1 and adjust the phase again if needed ? The audyssey in the denon has given me some different results each time I ran it as far as the crossovers and the sub distance which then changes the frequency response I had gotten with the sms-1 before running the audyssey auto setup.

Thanks,
Brian