Funny - I was over at Axiom yesterday filming a video of Andrew Welker talking about this exact subject! **spoiler alert** He suggests in the video that you get each subwoofer sounding great on its own in the best spot for it in the room, and then you hook them together. EG calibrate each individually, as a single subwoofer, and then get the splitter out and do final tweaks from there.
Of course Andrew's suggestion is good but he is essentially saying to manually position and tune each subwoofer rather than use an automatic calibration like Audyssey or MCACC. The op was asking about using the MCACC automatic calibration that is a feature of his Pioneer receiver. Like Audyssey, MCACC will attempt to correct for room-related issues like modal points. It also sets delay and level for each speaker. I would use this for the other speakers only and then follow Andrew's suggestion for the 2 subs. Probably this could be accomplished by setting subwoofer as none before running MCACC.
