You shouldn't be painting into the atlas or otherwise manipulate large textures like that - they will be duplicated in memory and can end up costing a lot of ram, but you can if you really want to. Also, if you were painting into something like that you probably don't need to use an atlas for that - its a very roundabout way of doing something for no real gain, just use a quad with a texture / render texture on it and draw into that - the uvs on that should be 0,0..1,1