Call me crazy, but I still kind of think that the two sets of eyes fuse when an Uchiha gains EMS (meaning that Sasuke wouldn't have any "original eyes" lying around somewhere, and that his current eyes would be a fusion of his own and Itachi's). As for how they fuse, I don't know. Perhaps the Uchiha have some kind of method to merge the eyes on a cellular level or something like that.
I think this because it was stated that Uchihas killed their siblings throughout history to take their eyes, but if it really is just simply transplanting (and not fusing) eyes, then why wouldn't the siblings just simply make the trade instead of killing each other? Over all, I just don't think Kishi would make it that easy to gain EMS. That is seriously way too easy!
Either this would have to happen, or something would have to happen to dispose of the original eyes if it isn't a fusion.