quick question, I know I should know this one, but can't remember and don't have my books handy.

R2, RH pitcher going from the stretch. He comes set and the runer heads to third, pitcher was oblivious to what is going on behind him. He balks to thrid base, I call it, partner calls it at the same time. We give the award to the runner whos now standing on third, he goes home. Was the proper award given or should third base been the award considering runner was originaly on second when the pitch "began"?

Award third base.

Not to hijack, but this brings up an interesting point...if the pitcher does not disengage with R2 and makes a move to 3RD, is that making a throw to an unoccupied base since there was no runner there to begin with? Obviously if he steps off there's no problem.

It's legal for F1 to throw to an unoccupied base if it's for the purpose of making a play. Under OBR, "making a play" means that the runner is trying to advance. Under FED, "making a play" means that a runner is trying to advance or has feinted an advance.