After using the auto calibration and trying it with those settings, I like to break out the radio shack sound pressure meter and a tape measure. Then I check crossover points against speaker specs, double check distances, and reset levels. Since I live in a house I want all of the levels the same. For example with my speakers I'm able to cross over my mains quite low (40hz), but my center needs to crossover over at 80hz. I set the crossover for each speaker at or just above the low end of the speakers' rated frequency response and then do a reality check with my ear. Then I like to go back and do a phase check on the sub using a pure tone at the crossover point for the mains, followed by another listening test.