take off the door panels, there will be a few screws, one behind the handle and one in the side little pull thing (plastic) sorry i dont know the name. Pull the panel off starting from the bottom. Unclip all the electrical parts and take off the panel. You will be able to see about 4 or 5 clips on the door. Unclip them. Be careful because that plastic part can bend really easy and mess up on you if you ever want to put it back on. There will be empty holes now where the clips were. Take a small punch and dent in each of the sides of the holes. Not to hard you just want them in a little to make it easier for the next step, and not to have any hard edges.
The next step is covering the holes. Apply kittyhair to the back of the holes. Kittyhair is fiberglass in a can---read instructions. The kittyhair will oozze out of the holes in the front. Allow 20 mins to harden then sand. When you are sanding you want to feather edge the paint around the holes that you just covered. Use 180 grit paper to start with. When sanding you should see the levels of paint...bare metal, primer, then paint....kinda like the rings of a tree. Use a paint stick and wrap your sandpaper around it so you dont make pits. so once you have the entire surface smooth and its all the same height apply the bondo and do the same thing. It might take you a few coats to get it right. Once you get it smooth with the 180 go to 200 grit paper then finish with 400. After you are finished with that step you are ready to paint.
Clean the surface with a degrease/oil cleaner. wipe on wipe off. prime the area. wet sand with 400 grit paper then paint and clear and you are done.
Let me know if you have any more questions. ill look for some pics later