There are multiple ways to repair floor rust, but as for as I'm concerned there is only one right way:
Cut out ALL the rust and weld in a patch
Other options are
Sheet metal screws
The above are easy and convenient, but are not permanent and will hurt the resale if you plan on selling it in the future. The best way to remove the rust is with an abrasive cut-off wheel. They make an adapter to attach them to a drill. If you have never done anything like this before I suggest you read lots of articles, ask friends for help, or take it to a body shop. Itís a great feeling to do it yourself, and if you go that route take your time, and ask questions as you go.
Good Luck and have fun.