To eliminate rust you need to remove it. Cut out all of the rusty metal. Make sure you go a couple of inches farther than you think you need to. You do not have to use the whole floor pan, cut it to fit the damaged area. Pay attention to where you are cutting. There are braces under to floor yhat you don't want to cut into much. The floor pan is spot welded to these braces and it is a but of a pain to get them seperated.
The best method of installing the new metal is to weld it in.