It does the same thing texture painting does and paints over the top of any previously assigned images - wither those are bitmaps or Blenders own 'blank' maps. Any changes would then have to be saved. It basically means if you had four separate meshes joined for the sake of painting, whilst you're doing that the process should be painting the respective parts of the overall map to the individually mapped areas (the four separate UVW maps) of each sub-component. You can kind of do this already without necessarily using the projection painting tool as all that does really is allow you to 'paint' directly on the mesh using several localised source images from within Blender, which obviously helps where tiling issues are concerned.
