OK, so I've done the Auto EQ in both stereo and dual mono (2 channels), and I much prefer the results using stereo mode. Frankly, the results in dual mono just sounded plain bad.
So, I'm using the stereo Auto EQ results as a baseline, and I'm tweaking from there, as I wasn't all that crazy with those results either.
I remember reading in the Audio Control manual, which is one of the best and most entertaining manuals I've ever read, the author wrote that after the user spends significant time getting a flat frequency curve, the user will likely find that the sound sucks...and the tweaking will commence.
That author was correct, IMO.