sms-1 with audyssey multeqxt setup?

Hello all, I have a question on setting up my Denon 3806's auto setup when using a sms-1 also. Should I unhook my main L and R channel speakers first then eq the sub with the sms-1 or leave them connected and eq with the sms? Also, after I run the auto setup is it ok to adjust the phase on the sms-1 ? Im just really confused hear on the order to do all this because I dont want to screw up the results of the audyssey eq any. I have ran the auto setup a couple times already and got a couple different results as far as the crossover settings and the subwoofer distance audyssey set which in turn messes up the frequency response I had set before with the sms-1 ... If anyone else has a sms-1 with audyssey that can help me out or anyone that knows the best way to do this im all ears ....

Thanks,
Brian

anyone know about this??? Ill try the subwoofer forum also.

ok, thanks kal! I do use the manual on the sms-1 cause I too agree that the auto on that is not so great. I have had the sms for awhile now but its the 3806 that is pretty new. I am also new to this auto setup stuff so I wasn't sure if after I ran the audyssey I could then go back and adjust the phase on the sms-1 without messing up the audyssey settings. It seems that after I eq the sub with sms then run audyssey it changes something in the x-overs or the subwoofer distance which then makes the frequency response skewed. So...do you think its ok to adjust the phase on the sms-1 after I run the audyssey?

Thanks,
Brian