Once you have the best placement in the room for the subwoofer and have it level matched with the rest of the speakers, then you can mess with the phase. At this point I ran some test tones (Rives Audio test CD, corrected for the Radio Shack SPL) and got out my Radio Shack SPL meter. I ran through the test tones from 20Hz up to about 100Hz (my crossover is set at 80Hz) and noticed that one of the two settings had a flatter frequency response close to the crossover setting, so that is the phase that I chose. I can't remember if it was 0 or 180 degrees. But, there was a big difference in the numbers going from one to the other in my room. I've also read that you put on some bass heavy stuff and choose the one that sounds the loudest, or something but I couldn't notice much of a difference, with my ears. However, there was a big difference in how one or the other measured, in terms of a flatter frequency response near the crossover, which determines how well the mains and sub are integrated. At this point you could run Audyssey or whatever room correction EQ you have in your AVR. I think that you will get the best EQ results when everything is in the best location and such before you run the room correction EQ.
