I did online check-in for a combination room-only/package/room-only stay at the same resort (Pop). I had already had our reservations linked when I made them. When I did online check-in for the first reservation, I put our estimated arrival time. For the 2nd and 3rd, I put 7 AM as our arrival time. I did all the online check-ins at the same time. When we checked in the first night, I made sure that it was in the computer that we had a continuing reservation for the next 2 nights and that we were slotted to stay in the same room and the CM said we were. We had zero problems.
I figure if you're staying at the same resort in the same level room (standard, preferred, etc), there's no good reason for them to move you - it's more work for them to have to clean your existing room to get ready for a new guest and make sure a new room is clean for you, than to just have one room ready for a new guest.