If it is rusting between panels than a section of one of the panels needs to be cut out to access in between, sand blast the rust out and patch it. Most of the time with rust you can not properly grind/sand all the rust out, surface rust maybe, but if there is any pitting you will not get it all (rust still left in the pits). Sand blast and acid wash should remove all signs of rust for the safest repair.
No fiberglass whatsoever should be used to repair rust. I hate it when I see rusty floor pans and patches covered in fiberglass. If there is any rust under the glass it will pop the and break the fiberglass repair. If it was metal to begin with, fix it with metal, if it was fiberglass to begin with than fix it with glass...