If the holes are really small you could just use a stick welder and lay down a few beads over the holes and grind it flat (from inside the car). Then just seal it really well and spray some paint and ruberized undercoat. Make sure you get all the rust in the area completely removed. If the holes are really big, there is no way around it. You will have to cut the whole area out and weld in a new panel. I had a golf ball sized hole in my back seat floor in my MK3, and I just did a quick fix because it was the dead of winter and I figured I would fix it right later when I had the time. I removed all the rust in the area. Then I sprayed a primer sealer over the bare metal. Then I took a junk license plate I hade laying around and glued it to the floor using a liberal amount of roofing sealer. Next I screwed 4 short self tapping sheetmetal screws through the plate into the floor. I coated everything in ruberized undercoat (inside the car and underneath). Once it all dried I just put the carpet back. Its been a few years and I still havent gotten to fixing it right, but it has held up perfectly.