Bondo is a brand name. They make different bodywork materials (putty type fillers, fiberglass fillers, fiberglass resin, fiberglass matting and cloth).
You first need to figure out what way the rust is coming through. Most rot I've seen on cars starts from the backside and works it's way to the outside of the panel. When a hole appears this is one the tip of the problem. The area next to the hole can be paper thin and the thinned metal can extend back a few inches or more depending on the damage.
Ideally, cut the rot all the way out, weld in new metal, and then protect the backside AND frontside of the metal.
If I were to do a temporary repair I would look at the Bondo brand of filler that has fiberglass strands in the filler. I got a can out of the garage and on the label it's called "Bondo-Hair". The features of this mix is it is waterproof and since it is a different mix than the regular filler from the same company it will be stronger and offer more reinforcement to the repaired area than their regular filler.
Like any filler you need to rough up the metal and after you get it roughed up you may want to dimple in the metal slightly.
I've used the Bondo-Hair before on spots on my car and at work on sub enclosures and it takes a little more work to get the cream hardener to mix into it but you definately need to mix it well. Once you get most of the area you want to repair filled and leveled with the Bondo-Hair you can come back with the regular filler as a top coat.
Jim
