At a guess, I'd say it works like you'd expect, with one set of data being for regional and another being for national. One thing I do know is that you can't have any duplicate entries. That can cause crashes or simply cause the dex not to work properly.
Oooohh... It's that bad. If that made you cry, it really IS bad.
I'd post an image of what I'm talking about but I can't post links yet :/
Actually, I haven't seen anyone hack that animation yet except the Logo where it says "GAMEFREAK". That's why you haven't seen any tut around here did you? The only thing we can do about that right now is skip it.
Oh and try using Darth TME for creating your tilemap. Maybe that can help.