I reran the YPAO and this time paid more attention and looked at the manual as well. Once done you can view the settings it makes. I can see the frequencies for each speaker and size. Funny thing is it set my crossover to 160 and my mains to Large.

I'm not sure if I can skip any of the settings. WHen running I only see Exit which I assume cancels the entire thing.

If I change my crossover to 80 now and leave the eq settings I assume that would cause a problem because the eq is based on using the crossover of 160 for my center and rears. Or am I incorrect since the rears wouldn't use the eq all that much. Not sure how that would affect the center though.

Here's what I got for my main speakers. Have no idea what any of it really means though.
Front L
1: 63Hz--- -1dB
2: 250Hz--- -0.5dB
3: 400Hz--- -1.0dB
4: 630Hz--- +1.5db
5: 1.3kHz --- +4.0dB
Front R
1: 63H --- -6.0dB
2: 79Hz --- -1.0dB
3: 320Hz --- -1.5db
4: 500Hz --- +3.0db
5: 1.3kHz --- -3.0dB
6: 13kHz ----1.0dB
7: 16kHz --- +3.5dB