Ah yes... the 'correct' solution.
The right thing to do is to take it into a body shop. Have all of the offending rust and paint removed, and sand it down to bare metal in the surrounding area. Then have a patch welded over it, and the entire edge of the patch well sealed. Then treat the area with POR-15, and color paint over it.
This route is difficult and expensive however, so most people do not pursue it.
I forgot to mention in my above post, that you should use POR-15 over the fiberglass patch and over the surrounding metal. It is an epoxy based paint and is VERY tough and VERY rust resistant. You can then paint color overtop of it and it will be almost invisible, especially with the battery sitting ontop of it