Just like using REW with a calibrated microphone, the Yamaha is not reliable at setting the best delay/phase setting at the low frequencies a sub operates at.
Run REW with the mains and subs together, adjust the AVR distance setting for the best frequency response. When you're off, you'll see sharp dips.
The AVR setting won't necessarily be the actual distance.
REW can also be used to set the delays on your other speakers using an acoustic timing reference. But, you'll need to do it at a higher frequency range than what a sub sees.