ParadigmDawg is giving you good advice. YPAO is, from my experience and from reading about other people's experience, good about distances (delays) and levels, but not so good about large and small and crossover frequencies. Fortunately, what is hard for humans to do well, it does well, and what is easy for it to do, humans often screw up. So follow ParadigmDawg's advice.
After setting things manually as suggested by ParadigmDawg, I recommend that you rerun YPAO yet again to make sure it does not change anything based upon the changes that you made. And then make sure that the crossover frequency has not been changed.
Basically, YPAO can be trusted for levels and delays, but not for crossover frequency (neither can other brands either, so you will not get any benefit from getting away from Yamaha, which I highly recommend and use myself).