Michael, a couple years ago I assisted a colleague in setting up his new system that included a Yamaha receiver with YPAO. The calibration part of the system(setting speaker levels and distance delays)is fine, as is typical with the auto-calibration available on receivers these days. Don't be surprised if the subwoofer distance shows as greatly different from the actual physical distance, since there are various delays which are being taken into account. One change that you might want to do is to skip the auto size and crossover setting procedure and instead manually set all speakers "Small" with probably an 80Hz crossover.
The other part of the system besides calibration is the room equalization. This is more controversial and the Audyssey system, as Randy points out, is widely considered to be superior for that purpose to YPAO. Nevertheless, we found it to be useful, using the setting to emphasize adjustments to lower frequencies(available on that model Yamaha)and you should certainly fully experiment with it when you have some time.
