I think the software-based approaches like Audessey are evil. For the few people I've helped with HT systems, I always think the "small" settings are worse unless you have stand-mounted L-R speakers. For as much as you've invested, I would spend another $300 on OmniMic, set everything to large, measure the system at your listening seat without the subs, and use the SB16 equalization to augment and fill-in where the L-R speakers are deficient or suffering from suck-outs from their placements, which is probably just below about 50Hz. For music systems you might want more equalization up to 100Hz or more, but I think that's probably a waste of time for HT.
Or you can continue fighting with Audessey...