They have their own check in - there are usually a couple of people at the desks in the lobby (where the Mary Poppins penguin fountain is) and you just sit at the desk for a moment while they check you in
If you get the villa number texted to you, you don't even need to stop at a desk, but so far checking in at the VGF I've had to chat briefly w/ the check in person to get my room number and confirm the cc on file.