Ways I've done it (but it's been a long time):

Method 1
1. Weld hole
2. Grind off excess
3. Bondo

Method 2
1. Tap a small ding at hole site
2. Bondo

How ever you do it, you need to have some skills at body work or it will look wavy after you paint. I can't tell you how many vehicles I've seen with good paint but wavy lines from a poor attempt at filling molding holes. If you can feel any waves or dips at all when it's primed, it will be glaringly obvious when it's covered in glossy paint.