If you are not satisfied with the "Normal" MCACC auto set up, try running the "Expert" or "Pro" MCACC routines. I don't know off hand of any multiple sub settings in the normal MCACC set up in the Pioneer, but perhaps in the expert or pro menus.
The 84TXi, and maybe the 82TXi, allows, in the expert MCACC i think, an ability the take an average EQ across three different microphone placements. Perhaps that will help strike a balance with bass level if you separate the subs. I can't see this helping with phase correction though. Although there is the Phase Control feature in your receiver which is performed during the MCACC set up, perhaps it will compensate somewhat.