Generally a program like YPAO (or Audyssey in Denon/Marantz units) will reset everything when you run it. Some have the ability to save a calibration, some don't....can't say I've read about saving YPAO but my avr can save an Audyssey calibration (with a computer) but it's not the quickest process to save nor to put back into play.
Many of these programs will set speakers to large regularly even when you tell it you want to use a sub, as I am fond of saying that's because the marketing guys don't want to tell you your stuff is "small". General rule of thumb is not to lower a crossover below what the program suggests (and sets for eq), but raising the crossover is fine.
