Phase refers to the relationship between the sound from the speakers at frequencies higher and lower than the crossover region. I wrote 'region' because it's not actually a crossover 'point', it happens gradually as the frequency rises or falls, depending on whether the low or high frequencies are being filtered.
Sound is energy and a pure tone is created from a sine wave, music is complex and made from multiple frequencies which are produced at the same time. The energy from each speaker interacts physically in the air and the measuring/listening location make a big difference- if the mic is closer to one speaker than the other, things can go bad pretty quickly, or it can be better- it depends on the speakers, the room, the acoustics and the frequencies.
if the sub has a switch with 0° and 180°, you have two choices to correct this problem, usually wrong. It might be better in one position, but that doesn't mean it will be the correct position.
If you ran REW and saw a deep V in the response where the sub crossover is set or in the 60Hz-120Hz range, something needs to be corrected. You can use REW to send pink noise to the amplifier & speakers without taking a 'snapshot'- use that to SEE the changes in the response as you move your sub or speakers, change the crossover point(s) and rotate the main speakers. I would start by putting painter's tape at the front edge of each speaker, so you can return them to where they were, in case that ends up being the best place for them (you won't have to hunt for the best location again). I would recommend finding the best location for the main speakers first, with no subs operating. They're more important to the main sound because they're the ones that allow you to hear location of sounds.
