If you listen to it just the way Audyssey sets it, do you feel it's lacking bass even with LFE+Main compared with before calibration? How does the bass sound set to LFE and speakers set to small? Try comparing those with uncalibrated (Audyssey off, no EQ) to get a feel on which direction you want to go with bass (more, less, etc).
How do the mids/highs sound to you after calibration vs. before? Those speakers have a decent rise at the very top of the response--do you like the way they sound uncalibrated (lots of detail, etc) or do you like them better after calibration (maybe less harsh, etc)? This will give an indication of whether you want to limit correction to lower frequencies or if you like them better corrected full range.
Short of that, you could download the app and do a run with that. Then if you like, email me the file and I'd be happy to take a look at it and walk you through a few suggestions.