If there are only smaller area's and not any rot anywhere else i ususally just cut that area out and leave as much original sheet metal as possible. I cut up a new replacement floor pan to fit the area. The re-pop sheetmetal is not an exact fit and you have to work with it.
Depending how ambitious you are you can either butt weld or overlap.Remember that overlaps in sheetmetal can rust out down the road if they are not sealed up from water getting back in.