Different room correction equalizers work differently. But if you are only concerned about the response from one listening position, you should only measure from that one position. It depends on what result you are after. If I were you, I would try to follow the instructions for YPAO as they are written in the owner's manual.
That is a room mode, and it is a product of your room's acoustics. The only way it can be solved is either by moving the subwoofers or moving your listening position. Equalization will not fix that. Experiment with different subwoofer placements, or you can also just move your seating up a few feet.