I use Luxology's modo for the 3D work that I need in Second Life®, and have recommended this workflow to others as well.
One of the many things you can do in modo is paint directly on a model. However, painting on the SL Avatar can be tricky, because of the 3 material zones, and their overlapping UV Maps.
In this video, I show how to overcome those limitations by remapping the Avatar, and then how to start painting on it.
The problem is that the maps are superimposed on each other, since they are all named "Texture." This makes it impossible to paint on one map without the strokes also showing on the other two. The three materials also make it difficult to paint across them.
You'll need to have one map with all the UVs on it, for easy painting, and another 3 maps with to burn the textures back to the Linden map for uploading to SL.
Fortunately, it's easy to make them. Just Copy/Paste the UVs to a new map, and then use Pack UVs to spread them all out.
Then, select the polygons that are in each material, Copy the associated UVs, and Paste each of them into a new map, as well.
When you're done, you'll have the original Texture map (might as well keep it, just in case) and 4 new maps. Call them "All", "Head", "Upper", and "Lower".
Save the model as an .lxo file, not an .obj, or you'll lose the maps you just made.
To paint on them, make a New Layer in the Shader Tree that's an Image Map, and choose a size that's at least 2048x2048. Then go to the Paint tab, choose a brush, tip, color, and nozzle if you're using a graphics tablet, and just start to paint!
When you're ready to save for SL, add a new Image Map layer at the default size. Make sure you are baking to the correct map by going to Properties, and choosing the desired UVs from the Texture Locator tab, under Projection.
Then right click on the Image Map in the Shader tree, and choose Bake from Object to Texture from the drop down menu. Accept the defaults, and it'll bake the texture you need in SL, just like that!
Save the image from the Render window, and you're ready to repeat for the next one!
For more detailed instructions (including where to find all the things mentioned) watch the video.