It depends on the leather. Also if it is real leather and not pleather. If it's real leather, you don't need to strip the paint, you just need to break down the surface with acetone. Then it should take dye. there are a few circumstances where a real leather won't take a dye, but the likelihood of this happening with shoes is slim.
If they are pleather, you will either need to paint them, or use a permanent marker. I'd suggest the big, fat Magnum marker. They are a little less purple-y than the Sharpies, and a lot larger marking surface. Then you shoe polish over them to knock down the marker tone.