My heat shields are installed under the frame rails as well. I have one big horse shoe shaped one under the rails that comes up under the engine tins and is sealed with a similar seal as the VW Bug.
Then, I have another shield on top of the rear portion of the frame rail that seals that area between the rail and the rear inside of the body. That piece has a kip-up at each end to seal just beyond the tail lights. The two, together, are pretty effective.