Is there a problem with letting YPAO set your levels and delays? I think at the most basic level, that’s what all room correction software gets “right.” At least with Marantz and Denon running Audyssey, you can turn it off and preserve those settings.
For the sub phase, I would always start those off at zero. Having a friend’s assistance is great for this. Sit at your LP, playing a good bass track through your subs and have your friend turn the dial on one first, then the other. Your goal is for the bass to sound the best at your LP,. Cost: a six pack.
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After all of that, run YPAO again to confirm everything.
Then, at least with REW, you can play your test tones through your AVR and calibrate the levels to the appropriate Reference Level SPL to suit your taste.
I have not used REW to either check phase, or to program a DSP like the 2x4.
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