Finally got my in-wall surrounds installed and ran YPAO to calibrate all the speakers. Worked great at first, but I noticed later that evening when watching TV that the sub (MartinLogan Dynamo 500) wasn't responding. It took me a full day of trial and error messing with cables and fiddling with settings to figure out that the YPAO set the LFE output super low to -10db (the maximum downward adjustment) to compensate for what it thought was too much bass during calibration. The problem is that, like many powered subs, the Dynamo will power down after an hour and won't turn back on unless it senses a signal, and -10dB was too low to trigger the Dynamo to turn back on. Making matters worse, the sub worked fine just after the initial YPAO setup, but only because it was already on and didn't power down until a couple hour later, so I didn't occur to me that the YPAO was the culprit. I set the LFE output level back to 0dB and the sub came right back on. From there, I just adjusted the volume on the sub itself to get the bass level back to where it should be.
Apart from that, YPAO seems to have done a good job with calibration - it's no Audyssey MultiEQ, but it does a lot of the initial grunt work well. Just beware that if you have a sub has a power saving feature, make sure YPAO doesn't set the LFE output too low or else it your sub may never come back on because it can't "hear" the LFE signal.