Depends on how you want it to look and last. If its a farm/work truck I take a sledge hammer and beat it close to straight and weld new metal in as necessary. Wire weld distorts the seams less than braising but have ox/acetylene but not wire yet so I use that and beat it back flat and reweld as necessary. Not pretty but it works and mostly doesn't break there again.
Putty (bondo) tends to crack and come off after a while in rough service, off road conditions, and from what you have said about your road... :no:
Fiberglas would be a stronger, more durable repair and will not be affected by water. Just make sure that where it is applied over metal to remove ALL rust and leave only bright shinny metal. Bit harder to work with than putty but it's good for floor pans, door panels, fenders and such in Jeeps and trucks that are prone to rusting out.
My 2 cents worth
