I would use a drill bit.
I really don't think you'll have to worry about messing up the paint. If it's a good paint job, nothing should peel up. Start with a small drill bit and then go up to the desired finish size. If you want to be sure the pilot drill bit doesn't wander, take a larger sewing needle and use it like a center punch to make a dimple in the body. Some guys lay down some masking tape before marking and drilling holes as well, but it makes it harder to see if the holes are where you need them.