it also depends on current overall condition and desired outcome.
busdaddy covered it pretty well...at the very least the metal that is to be welded should be cleaned well (wire wheeled/grinded) and prepped and weld thru primer can be used in any areas that will be lap welded together (cross members and area of cargo floor, etc). with the old floor removed everything will be exposed and it will be a great opportunity to clean, prep, prime, paint other areas (frame rails, cross members, cable guide tubes, etc). rust mort/rust inhibitor, master series primer/paint, por15, or similar products could also help preservation of these areas as well as all the new metal going in! just my $.02