Trey, first as to location for your EP500, except in a square room, generally the best location for a single sub is the tightest corner(farthest from a large opening)behind the speakers.
As to the "crossover"(actually just a low-pass filter)setting on the EP500, depending on what model sub amp you have, set it either to bypass(if available)or the highest frequency to get it farthest out of the way of the crossover that the 659 is doing.
Although you mentioned that you also used the "built in test tones" on the receiver, it's unclear if you meant that you used them as part of a manual calibration or if you used the 659's auto calibration. If you didn't, I'd suggest trying the auto calibration rather than going through the complexities which you've described.
