Alright, I've spent some time playing with the thing, but clearly I have a lot to figure out. I did a RTA room correction analysis, and it sounds OK, but frankly I'm not all that impressed. Maybe I just need to fool with it a little more.

I do know I'm still not dealing with the bass end properly. For one thing, the default setting for the RTA AutoEQ is to ignore everything below 100Hz! The manual says:

It makes sense to exclude the low frequency range (up to approx. 100 Hz) from AUTO EQing, because it is this range that may produce inaccuracies during the calculation of the frequency response, which might impair the results achieved with the AUTO EQ.
But this is the frequency range I'm most concerned about!

Also, it seems to be doing some fairly dramatic corrections on the low end right above 100 Hz. Two adjacent frequences are very different, one correct +7db, the other corrected -7db.