The key is to make sure that the two rooms you want credit for get put on the same folio (one bill showing charges for both rooms). I've had experiences where I've booked two rooms on the same reservation but the hotel split the bills so each room had its own bill. That will result in earning points only for the room you were in. Easiest to get this fixed before you leave the hotel. If the rooms are billed separately, get them to combine them before you leave.