Originally Posted by eugovector
Not knowing a whole lot about your particular setup, I'd set everything to small and adjust your crossover as low as it will go.
This is good advice from eugovector, and a fine starting point. The Yamaha's YPAO is sometimes wrong and only offers suggestions, in any event. Leave all speakers set to small, but I would suggest setting the crossover at 80 Hz. Those surrounds won't go much below that and the Yammie doesn't set individual speaker crossovers. (There is only one xover for all speakers.) Try it at 60, as well, and see how that sounds to you.
Ultimately, you may want to acquire an spl meter (Radio Shack, analog) and a Rives or Digital Video Essentials disc for finding your system's/room's actual frequency response. The flatter, the better.
Good luck with the setup. You'll enjoy your rig.