I'm still thinking that I'll need to unplug the stereo inputs during the Audyssey sweep test cuz as it tests the fronts the subs will come on should the subs be connected to the stereo preamp. And although it will think the mains are very deep, it will trya nd do a time alignment and possibly implode (assuming sub isn't in same time plane as mains). I will, however, try your idea to have the sub(s) EQ'd and the SMS in the path so when the Audyssey sub/lfe channel test comes up it hears an EQ'd signal.