JH, I also was a bit confused about what you meant by "off" and "same" in describing your results. In any case, for the setting of speaker and sub levels you can rely on the auto-calibration part of YPAO to do a good job, at least as accurate as would be done by a manual calibration using a test tone disc or the receiver test tones, aided by a SPL meter. If the resulting sub calibration, although probably accurate, isn't loud enough to satisfy(e.g.,"paid good money for that sub; want to hear it"), then it could be manually bumped up 3-4dB.
