Since this tread was created I've had a little bit of a change of heart regarding YPAO. I would say 80 to 85% of the time I don't use it. I never use "Flat", that is entirely too bright. "Front" is just null and void to me as well. "Natural" , I'll use sometimes depending on the recording. But most of the time I use "Through" (No Eq at all) That just seems to sound the best to me, most of the time. When I ran YPAO, I set the level on the sub a tick or two past halfway, and If I remember correctly YPAO set the sub level to around -1db. I bumped it up to about +3.5db and it sounds pretty good now. Yamaha also has something in the option menu called subwoofer trim. Although I'm not sure what that does. Natural setting sometimes seems to create a tighter image and more defined soundstage, if that makes sense. But most of the time Through just sounds right with most music.
My biggest thing right now is deciding if I should get a second sub. My room is small. About 13' across and about 17' deep.