cut out the rusted part.
remove paint as needed and then fibreglass/glue/weld/epoxy/seam sealer or otherwise attach the new piece of metal into place.
use seam sealer to seal it up
repaint

look here for an example. in this case he is tubbing wheel wells for more clearance. but the idea is similar.

85 runner -dual cases, headlight harness, 34" TSL's
86 toy buggy getting sas'ed with a 14 bolt rear - 8.5" 10 bolt front (this will go away when i find a 60)