Hi . . . this is an old thread, but did you figure out what to do . . . simply run YPAO, then afterwards manually set ALL your speakers to small, even if you are using large speakers. Remember to set your subwoofer to it's highest setting before running YPAO, if it's a yamaha sub that will be around 140 or 150.
I must say, however, I have found that sometimes, not all the time, YPAO does NOT set the AV bass crossover at the best point (and I am a die hard Yamaha AV receiver fan). Therefore, when the YPAO set up is complete, manually set your crossover in the Yamaha settings to slightly higher than the lowest frequency point of your satellite speakers (it might be that YPAO got it right, but if it didn't, change it). For example, If your speaker's low end is 100, then set your AV crossover to 110. If your speaker's low end is 60, then set your AV crossover to 70. Easy.
This will will send ALL the base and LFE sound that strains your speakers to the subs, and better harmonize your sound-stage. Will it be perfect? No, it won't. The only way to get it perfect is to do the speaker calibration with a hand held sound meter (you can purchase one at RadioShack). But it will be much better than running your Yamaha receiver with the large speaker settings . . . as a general rule, you hardly if ever, run your AV receiver with the speakers set to large . . . if you do, your sub does little to no work, and minimizes having a dedicated sub for lower end sound, and places the strain of the lower end sound on the other speakers.
Think of it like this . . . it's like owning a pick-up truck and a minivan, and you opt to haul 90% of a heavy haul in the minivan, and the remaining 10% in the truck, instead of just putting 100% of the heavy haul into the truck, which is designed to do the heavy lifting. Even though the minivan can do some of the work, it doesn't do it well or efficiently, it really isn't designed to haul heavy loads, but the truck is. So, while the minivan can strain to do the work, the truck can do all the work without the strain. And the minivan ends up lasting much longer, does not have wear and tear, damages, etc. As to the truck . . . it keeps on going, too, since it's doing exactly what it's designed to do. The truck is heavy duty, and it will take an enormous amount of stress, or overload, to damage it!
Like the minivan, all speakers can handle the stress of some bass sound, but they can't handle all of it (well), or at all. Therefore, send all the bass sound to the sub(s) (two subs are better than one), even if you have LARGE speakers . . . let the dedicated speaker (the sub) do what it is designed to do, the heavy (or low base) lifting! It's the pick-up truck in your speaker system . . . and rarely if ever can you send so much low end sound to it that it can be damaged (well, it can be damaged, but you'd need a tremendous low end thrust to do that, and in a common Yamaha AV unit, you need not worry about this).