[Stiglr]

Not sure if I understand you properly...

but it would seem that any layer would be a version of the texture file made from the basic UV map you create before beginning texture work.

You'd make a file from a copy of just that layer in Photoshop/PSP/Gimp/whatever, and set it up for its end use (selecting or deselecting alpha layers as necessary, as one example).

So, you'd have a texture/"paint"/"skin" file (which itself might have any of dozens of layers for best visual results), a bump map file, an occlusion file, perhaps a damage file. But they'd likely all come from one layered .PSP file, and you'd mix and match the layers you want to create the files you need.