There should be no difference, really. Jump in and give it a shot. If you run into a specific problem, let us know what program you are painting with and the problem you are having.
Painting might as well be called layering. I am gathering from your response that you are trying to paint over a .tga file or flattened image with just one layer, correct? Are you trying to convert a G2 template to aNHRL template? If you want to transfer a paint from a flattened image to a layered template then you must decide what images/decals you want to keep and "cut" them out by using the free hand selection tool by carefully tracing around the decals. You can then place them on the new template.