When the 976 runs its levels/distances/phase adjustments will it adjust for phase on each sub channel?

Sorry if I am beating a dead horse here just trying to get a few things clear in my own head. We run our sub on a side wall firing across the room. When we moved, the sub went to the other side of the room with poor results. After posting here it was suggested to try flipping the phase switch on the back of the sub (cheap sub). Adjusting the phase corrected the issue.

If we had a sub on each side wall I can see where it could be necessary for the phase setting to be different for each cabinet. Could something like this be an issue or is my thinking on this wrong?