All "large" means is do not use bass management. "Small" means use bass management. I'd also start with an 80hz crossover, but experiment above and below from there, it's generally fine to raise the sub level after using something like YPAO or Audyssey, but don't go below their recommended crossover as that generally means no eq below that point. They have powered woofers, but you'll have to decide how to utilize them if you're going to feed them a sub pre-out (or not), multiple bass output points may help, might be better to use sub alone. Experiment. Not everyone likes the way a setup system like YPAO will aim for flat bass response, many do like to up the sub level, but do it in the avr, not on the sub itself; when an avr says try the midway point on gain for external sub amps, it's simply a guess. Yamaha doesn't have you set levels for sub separately from speakers IIRC, so you might want to do that separately from YPAO with an spl meter. What are the trim levels set by YPAO for your speakers and sub? (before you changed anything)
