Yes, it will work the same as booking a resort directly through Disney. You can go online or use the my disney experience app to go through this process. Please note that the Grand Californian does not offer this service.
We would recommend going to the check-in desk upon arrival though. They will give you a welcome packet and make sure your contact information is correct. Once your room is ready (if not already) you will get an e-mail or text message when it becomes available. At that time they will also give you the room number and area the room is located.