Drilling holes in the metal for the bondo to adhere is not a good idea. It will absorb moisture from the backside, rust under the bondo, and eventually pop off. I would grind it out now, and spot weld the holes in, grind it smooth, and put a thin layer of bondo, or glaze over it. FYI all you need is to hit the area needing filler with some 80 grit sand paper. What filler are you using? Looks like the pink Bondo stuff. There are alot better fillers out there these days. I really like the Rage Gold, and the Rage Extreme fillers from Evercoat. Looks like you are doing a pretty good job, and I would hate to see you have problems in the future, that could ruin your nice pait job. One other thing before I get off my soapbox, run your fingertips accross the panel, and any indentations, or anything that your fingers feel WILL show up when the final paint is applied whether you can see them with the primer or not.