There is no barrier to reserving two rooms with different check out dates. When you reserve you give a deposit for both and pay remainder by whatever schedule applies to your particular reservation (packages usually require advance payment in full a few weeks before; with most room only reservations you just pay when you get there). When you check in your credit card will be attached to each and you will need to check out of one and pay all costs charged to that particularly room on the first check out date.