I think you may find it very easy, but yes you do check out and in. You can go check in at 6AM if you want-that way you may have a room by the time you check out. We always split our stay, usually from VWL to BCV (soon to be BLT then BCV). Anyway, I go over to BCV early am and check in. If the room will not be ready, we check out at 11AM and bell services come up (we give a decent tip for that) and take our bags from our room over to our room at BCV. We simply head over to EPCOT, then back to our new room at BCV later. Works great.