The filler that you will want to use is called "Marglas" or "Kitty Hair". If the rust holes are really big (1" or bigger), use the "Kitty Hair" as it has longer strands of fiberglass in it that will make it easier to span the holes with the filler. If your looking at a panel that is just perforated with a bunch of tiny holes, use the "Marglas". Its a bit finer and will be easier to work with. Before you begin filling the holes (large or small), tap the metal around the holes in a bit so that the filler can be feathered into the solid surrounding metal. If you don't "countersink" the holes, the filler will only have a very small surface area to "grip" onto. Once you have the holes completely filled (Not even a pinhole should be left or moisture will seep in) it is OK to use regular "Bondo" type fillers for your final surfacing. Regular fillers are much easier to sand and make smooth than the fiberglass fillers. If you do a really good job of smoothing out the fiberglass filler and just have minor low spots or divots left, you might try using a 2 part polyester glazing putty instead of regular filler. Polyester glaze sands incredible easy and is generally very inexspensive.
These fillers are basically chopped up fiberglass suspended in resin. As mentioned, these fiberglass fillers don't absorb water like "bondo" type fillers do.

Provided that you treat or remove as much rust as possible, this type of repair can last quite a while. I've seen some last for many years before showing signs of trouble. The key is in killing the existing rust and using a water proof filler.