If you set the speakers to large, then the crossover is not used. I don't know why the receiver still lets you specify one (I have the same receiver).
As markw said, you really should set the sub to No. The only reason to set it to Yes (when speakers are set to small) when you don't actually have a sub, is if you want to reduce the amount of bass, maybe out of respect for your neighbors. Any bass that is redirected to the non-existent sub is lost. But as said, no bass is being redirected when the speakers are set to large, regardless of whether sub is set to No or Yes.