here's the order you should work in:
I am assuming the easiest config, which is all channels set to small, crossed off at 80hz in the receiver/prepro. All other sub adjustments in receiver and sub amp turned off.
1. find the location with the least nulls
2. experiment with port tune and room compensation (on SVS subs
3. manually EQ under a preset with only the sub playing.
4. now plug in the main speakers. The overlap area may be bumpy. Now play with polarity and then phase for smoothest response.
5. calibrate all channels' output.
6. play test material at increasing volumes until you get to demo/wife's-outta-da-house volumes to see if you can cause distortion. Those samples I mentioned above are the worst offenders in my collection. if you hear distortion or worse, clacking or some other mechanical noise from the sub, somewhere along the chain the output is too high.