Have you started yet? I've done a fair bit of rust repair with really good luck. My dad's 2003 Jeep Grand Cherokee had majorly rusted fenders which I patched up a 3 years ago (3 new york winters). They still look great with no signs of returning rust.
Waterproof, sealed, waterproof.... most important. Patch with steel, fiberglass, galvanized flashing, or whatever you want as long as it is sealed up and waterproof. Bondo and a few coats of rattle can paint won't last. If moisture can get to the back, it just won't last. If the patch material can absorb water (like most body fillers) it won't last.
My process for a low budget fix would be:
1. Cut or grind away any rusted metal. I grind back through paint that still looks pristine until I find clean metal. You will find that rust creeps along the steel under your paint before the paint shows any kind of defect.
3. Get some galvanized flashing from your local hardware store.
4. Cut and bend patches as needed.
5. Get some 3M body panel adhesive (08115). I don't use the mixer tips that come with the adhesive. You can buy the gun to squirt the adhesive, or just make your own. I have two pieces of broomstick screwed to a small board, and I shove those into the tubes to squirt some out on a mixing board. Mix the adhesive, and go to town. It's like JB weld, but a little thinner. It seals wonderfully, sticks great, etc.
6. Coat all the areas that you have ground down with the body panel adhesive (inside and out), and stick your patches on. you'll probably need some masking tape to hold the patches.
7. For small holes, just grind them down and fill with the body panel adhesive.
8. I would skim coat a thin layer of the body panel adhesive over the whole patch to further seal it up.
9. If you want, apply some waterproof filler and paint to make it look pretty (marine stuff is good). If your patch is all sealed up with epoxy (body panel adhesive), then further filler and paint is cosmetic only.
10. Spray 3m body cavity wax or Fluid film on the inside of the repair, and maybe even the outside if you don't mind it being oily.
This is a good patch that should last several years.
Lest folks should think I am a hack bodyman, I also do top quality body restoration work. You need to decide what you want. Honestly. welded patches don't necessarily last longer. It will cause paint to burn off inside your panels around the patch area, creating more possible places to rust, and many patches are welded in with some overlaps or gaps that trap water. I have cut apart plenty of welded in patches that created as much problem as they fixed. I'm sure it looked good and felt good for a year or two, but then things went down hill.