[Zero10]

JB weld is much stronger than bondo, and much less likely to crack.
My personal method is to wire brush the crap out of the area until all of the offending paint and rust is removed, then sand the area with 200 grit sand paper to make sure that the surface is uniformly rough.
Then cut a piece of fiberglass mat to cover the hole and any weak areas, set it in and brush a small amount of resin on it. Don't go overboard or it will be dripping into the footwell and ruining your carpet. Some people apply resin to the metal underneath then place the fiberglass over it, it is not too different either way.
If the thin areas are extensive then I will apply a second and/or third layer of fiberglass over the hole. Once the resin has set I will sand it smooth and paint it to match the rest of the car. After a day to dry and set I then re-install the battery.