mmm i don't use the 3D paint tool, but if you were to paint a texture in another program, like photoshop, then assign it to your model, it'd be very easy to alter. just make any changes you want in photoshop, save, and reload the file texture in maya. or save it as another name, and import that instead.

if you want to do it with the 3D paint tool, maybe someone else can help you.