Different properties will pre-assign their rooms at different times. Some block the actual rooms to specific reservations and others will just deal with categories leaving the actual room assignment to the FDC. And let's not forget the picky guest that requests a specific room for whatever reason.

If you're talking about two one-night reservations, then calling or emailing the property ahead of time is wise and make sure you confirm upon check-in. If you've got a day or two before the next rez then they should be able to handle that at check-in. Also make sure you request they code your key for the entire stay so you don't have to get a new key when switching reservations (I've found many FDCs don't know how to do this).