I used my panel flanging pliers a lot and really like them. Mine is just a driver, not a concours, so it doesn't matter if there is a seam where the factory never had one.
For filling, I used Duraglass, a fiberglass reinforced filler. Similar products are Kitty Hair, Gorilla Hair, and Tiger Hair. The stuff is strong and waterproof. I saved the standard body filler for the finish coat. I bought it all at a professional PBE store, rather than a Pep Boys, so I trusted their expertise.
Worked for me.
Does yours look like this?
http://www.homestead.com/chuckthetruck/page3.html