You have to make a separate material for every texture you want to export. Blender is really finicky about this (because 2.49 svcks, but we're stuck with it until they make a nif exporter for the new one), but you have to add the material in just the right menu or else it'll just replace the texture with the other texture.
So, you need to select the faces you want to apply the second texture to (in editing mode), and click on ADD NEW in the Link and Materials menu in the Editing Tab (not the materials tab, because that would make too much sense--doing it in the materials tab replaces the material/texture instead of adding a new one).
Then you have to go into the Materials Tab and click on the Textures Button. In the textures menu, you'll see the texture from the first material, and it'll probably have a number 2 or something beside it. Click on that and select "Make Single User" before you apply the new texture, otherwise you'll replace the texture on BOTH materials (because Blender is stupid).