Just weld in a new piece of sheet metal. Once that is in place and welded, grind the welds a little if needed so they sit level with the surrounding material. After that, you need to go get the fiberglass bondo. Its crucial that you use the fiberglass bondo as a base, before the actual bondo, to make it so the bondo doesn't expand or contract. The fiberglass bondo dries extremely hard, so you will be at it for awhile sanding it. Then after the fiberglass bondo, you can use regular bondo to make everything nice and smooth. Then shoot it with some paint of course.

I replaced a couple pieces of sheet metal in my engine bay like that, the pictures are in my build thread. I also have put body kits on numerous ricers in my area so I'm telling you the way i have done it everytime, and I have never had a problem. Its lots of work, not very expensive and comes out really nice.