I know a bunch of ways however none of them feel efficient enough for me. Currently I assign materials to faces and transfer maps from Maya, however this just gives me colors to pick with 'select colors', I'd rather have my layers all there. 3D Coat is also OK for it using per poly painting and it has layers and can export to PSD however I don't always have access to it and it's a bit time consuming.
Any other ideas?
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EDIT: Then for the rendered map, you can use my color splitter script in Photoshop:
http://www.martin.dahlin.net/downloads/NS_color_splitter.zip