I think Phase typically is left to 0 if sub is at front of room for initial setup. The setting you choose will always give an incorrect distance during auto set up- it is the dsp in the sub that is causing it. I've heard that you should leave the distance to what is listed during auto setup by some, others suggested changing it to actual distance. I can't recall how my ep500 is set right now, if you notice a strange delay in the lower frequencies you may need to adjust the distance. I'm not sure how this impacts audyssey as I don't use that feature of my receiver.
I'm sure someone more helpful will chime in soon
