What about those fun little border cases, where the character is say, right in the middle of 4 different 'areas'?

Well, you have access to the areas, so you can draw the intersections fairly easily. If you have something like:

1111222222
1111222222
3333*44444 <- player is *
3333444444
3333444444
[download]

it's just a matter of drawing the eight tiles for area 1, the ten tiles for area 2, and so on, with the right offsets. And since the areas are stored as arrays of tile indices (which, in OpenGL, are probably just texture names), rendering them is bloody easy (quads come to mind).

Are the areas actually stored as giant jpgs or what not, or just a reference saying 'these 3 thingies make up an area'?

I'd thought of the areas as n by n arrays of OpenGL texture names. Every time you have to draw them, you translate to the area's origin, then just iterate through the array: if a cell's visible, draw a quad with that texture.

"as well as a map of which areas go where" How the bloody heck do I do this?!

Well, you could use XML... ;-)

Seriously, it's probably easiest to have some notion of a grid, with one particular area associated with each coordinate. (This lets you reuse stuff, too: sort of like the tile grid for areas writ large.) So, you might have a text file that looks like:

0,0:plains.buu
0,1:plains.buu
0,2:rocks.buu
0,3:city_foobar.buu
...
[download]

Probably best to manipulate it with some sort of purpose-built tool (Perl/Tk springs to mind) rather than by hand, but you could create, say, a 4x4 test world by hand pretty easily.

You might find FlipCode and GameDev.net helpful, especially the fora.

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