I used a wire wheel cup brush on my rusty floor (wear a mask!!! this is dusty as all get out), treated it with ospho, and painted the clean metal with rustoleum primer and paint. As far as the bolt holes for the seats go, i just put a glob of seam seamer over the holes before i put my new plywood in, so that it would seal them up pretty good.
Keep in mind if your floor has any serious rust, you will have to spend the time to use an angle grinder to cut out the rusty sections of the floor, and patch it with new peices of metal. Some folks weld the new pieces in, but I just used some rivets and seam sealer around the edges and that seems to work fine.