The right way to do it is to cut the metal out and replace it. You can also get a cheap brake and a roller to make your own panels, if its not a resto, then they dont need to look stock. The tire well can be ordered. I have seen people replace the tire well with a flat sheetmetal floor with some beads rolled in it for strength, some box tubing welded underneath for bracing, then a fuel cell under the floor.
Then there is the cosmetic way. If the metal is basically good and you got rid of all the rust, you can fill some of the small pinholes with labmetal, sand it down and paint over it. SOme say its a crappy way of doing it, but if done properly and sealed from future rust, it could last a long time. I would limit it to a few pinholes though, if the panel looks like swiss cheese, then its time to replace it.
