The real fix is to cut out all of the rusted area and weld in a new piece. Barring this the rust can be ground or sanded out the best you can then chemically treated.
The link has a pretty good section on rust removal and repair. A Google search will turn up more hits.
http://www.knizefamily.net/minimopar/bodywork.html
There are some paints such as POR-15 that are supposed allow painting over rust and chemical stop it, but have no experience with this
The important thing is to eliminate as much rust as possible or it will just come back slowly. If you have rust in areas you can not access, try applying something like LPS-3 liquid spray which is a great rust inhibitor.