Bodypaint is undoubtably the best 3d painter on the market for handling multiple UV maps. For preexisting .obj models you Should import using the Riptide plug-in though so that you are preserving the material groups with multiple uv maps you need to create a texture for each uv map so open one of the materials on the first map and under color click on the arrow next to texture and hit create new texture, it will give you options for what size and color your texture should be. now go to all the materials which share the same map and go to that texture arrow and select bitmaps and you will see that texture select it. when you get to a material that is on a new map create a new texture for that map, and go on from there. the key is that you need a texture for each uv map.