I haven't had a chance to fully mull this over, but if you plan to use the SMS-1 in some cases and the Audyssey in other cases, the best bet is to put the SMS-1 in the signal path and leave it there, but to change it to preset 6 when running the Audyssey setup and when using the Audyssey EQ. Preset 6 is a "bypass" mode for the SMS-1, and as such applies no EQ to the subwoofer signal. You'll want to disable the crossover on the SMS-1 before you do any setup anyway.