YPAO definitely gets some things incorrect. For example, it always tells me that my centre speaker is large, when it definitely isn't, as it only goes down to 60 Hz.
Yeah, set all your speakers to small and crossover at 80 Hz to start with. You can adjust the crossover depending on what your ears like. With two powered subs, there's little point in letting any of your other speakers handle bass, so let the two subs handle it. That's what they were designed for.
cheers,
supervij