Bryn, is right on point in the above comment. Changing crossovers and speaker size after you run Auto EQ will not contaminate Audyssey's settings. In fact you probably should change them for best results IME. Usually changing all crossovers to 80Hz (except for mains in your case) and all speakers to small (again in your case the mains will be large because no sub) usually gives the best results. Give it a try and see how it turns out in your room, then tweak the settings to your preference if necessary.