If you have a 5.1 or 7.1 amp, you really don't want to use the stereo audio pre-out/main-in or tape in/out for the EQ! The reason is that the EQ will mess up the other channels which have normal speakers. You cannot use a tape out/in for the same reason.
Isolate the EQ so it goes to the 901's, and only the 901's. 901's w/o EQ or any other speakers with Bose 901 EQ would be far worse than using the TV speakers.
I believe most modern receivers have a pre-out (even those without a main-in), so if you want to try the 901's as mains (or surrounds), you need to buy a separate stereo power amp (ideally with a volume knob). Route the signal from your pre-amp FR & FL outputs to the Bose EQ to the stereo amp to the 901's. The main channel amps of the receiver will be idle, but unless you have a discrete main amp input for the front channels of the amp, I don't think that can be helped. AT least your receiver will run cooler than designed for

.
Assuming it works like Audyssey, I would expect the YPAO to work fine with EQed 901's. It doesn't know or care about the EQ in the loop, it only reacts to the sound at the microphone.