When we've had people join after initial reservation, we have always just added them at check-in. However, last October, I decided to join my parents on their trip. Since they were flying from Pennsylvania, I was going to make the trip solo from South Carolina. As such, we also weren't 100% sure that I would go until it actually happened. (I was nervous about the drive.)
Anyway, when we checked in, it was at Port Orleans French Quarter. Because there was a convention, they had done a complimentary upgrade to for my parents to a King size room, even though they booked one with two beds. It took quite some time to get everything situated because of the room situation. They had no rooms available with two beds, so they moved us to Riverside. The whole affair took close to an hour. I can't fault Disney, as they didn't know I was coming, but it made our night even longer.
Regardless, we had fun. Just keep that in mind if you're staying at a resort that could be close to full.
VelvetGloves