You can make your reservations at City Hall. They also have the menus of all the Disney-restaurants there, so you can ask to consult them first, if you want to be sure they serve something you like.
We usually make our reservations in the afternoon for the evening of that same day.
Once, we couldn't decide which restaurat at the NPB we wanted to eat at, and they made a reservation at both restaurants, and just told us to choose at the moment itself!