The best is to cut out the bad and put in the new. If you must here is what I have done in the past. Sand the primer but don't sand it to metal. It is good if the primer is 2 part epoxy. Put some nylon screen on the back side and hold it in place with masking tape on the front. Mix up some JB Weld and apply it to the back side and push the masking tape in from the front to dimple it down some. Let it harden, lightly sand and put another coat of JB Weld. After it is hardened use some bondo like material on the front and sand smooth. Prime with 2 part epoxy and paint. This is not a life time patch but if you removed all of the rust in the first place it will last for years. Again the best way to deal with it is a patch panel.
