Yes the pre-outs are confusing I don't know what the engineer was smoking it simply needs labeling to clear the confusion. I had to ask Onkyo about those too when connecting dual subs they said connect each sub to each pre-out.
I believe the pre-outs are tied together and not discrete separate channels. During AccuEQ calibration it didn't give me the option (not sure if it's supposed to) to correct phase for the subs like the Marantz Audyssey did, I believe the Marantz are separate for subs I only had it for a week so far.
Regarding sound quality comparison (music not movies) I can only describe the Marantz being very bright, controlled, and detailed. To be honest I was a bit shocked. On one rock song (nine inch nails or godsmack) the drums flowed across from left to right so clearly I could hear each separate tuned drum I felt I visioned the actual drummer and my jaw just dropped in awe, never experienced this before now I know why you guys are here.
The Onkyo steps up to the plate with movies not so much music, I tried various settings and music sounded more flat and contained like they were packaged/suffocating and not open exposed and bright like the Marantz. The Onkyo is still good sounding but something for me wasn't there.
I'm running SVS Prime Tower's up front, Martin Logan 8 center, SVS PB1000 dual subs, and Boston Accoustic surrounds.