If you are going to replace a section with part from a donor truck or fabricated from sheet metal the best way to attached is by welding it. Some have tried to pop rivet it in which works okay but it is not the preferred method.Be sure to clean the area of rust and treat the area with a coating so to prevent it from rusting over again.
Speaking of coating check out a site called
http://www.por15.com. It has a product that can repair a floor board with a coating similiar to fiber glass. And it permanently treats the area from rust, forever. It has some good write ups from restoration magazines.