Here's how I've started using Blender 2.77 to paint layers in 3d or 2d that can be exported as PNG files with transparency.
In this example I'm creating a layer so that I can add make-up to HiveWire3d's Dawn figure with Alpha and so that I can have a separate image of just the make up and not have to paint directly onto the skin texture itself.
1. Import your obj. For figures I'm in the habit of using "keep vertex order selected" and using materials to select specific parts while in edit mode. Here we have Dawn imported without textures
2. Preparing to paint.
Its going to be difficult to paint over the skin with those eyelashes in the way. There are ways to mask/hide such areas, but I find it better to just delete parts of the mesh I dont need
To do that, go into edit mode and deselect all (press a on Keyboard) and then using the material panel select parts that you don't need, here I have selected the eyelashes, all eye, teeth and inner mouth sections. You could also delete those materials if you wish to.
Then hit delete - Faces
optional - In the materials panel you can move the face and lips to the top of the list if required to ease selection...
4. Select your Face material , then in the textures panel, add your preferred Skin texture.
5. Select your Lips material and then browse texture to be linked and choose the the face texture.
6. Make the linked face and Lip material shadeless.
7. Switch to texture paint mode. The face texture should now be visable on the model but the materials with no textures might turn a distracting pink. If so switch viewport shading to "material"
8. Adding a new texture layer using Slots. This is where we add the new layer that we want to use to paint on.
So Click add texture>Diffuse Color
Click on the color (to the right of "color") and turn alpha (A) down to zero. Set the size to the same as your skin texture. You may change the name and also material texture panel to the same name and set "material texture preview" to show alpha there too.
9. Ready to paint! Click on tools and create stuff - next to blend it should say "mix". To delete change that to "erase alpha"
10. Save your new Texture as a png file through the UV/Image editor. I had trouble packing the image to the blend file so make sure it is saved through the UV/image editor to be sure you keep it.
Of course you can also do some or all of the painting in 2d using the Uv/Image editor depending on the circumstances. In 3d though, you could import a figure with the eyes closed for precision painting (not that I do much of that!)
Hopefully I havent led you round the world to cross the road.