The key on the sills is to stop the reason the rust starts, and this is mainly removal of the barrier cost I.e. The paint, once this scratched or chipped to bare metal no applied chemical will prevent rust, so first thing is to get rid of the rust or treat it, convert to a stable form etc. then apply a good base layer, I.e. Ecote, galv etc, then primer, then paint and top coat, ensure on theses parts you use plasticised coatings as they are more resistant to chipping, and for good measure add a protective film to the critical areas such as 3M.
On your internal panels once you are happy they are all painted correctly use waxoyl or similar, and re-apply periodically. I did this on my z when I did the wide body conversion, all the panels had to come off so I treated the whole under skin and inside of all panels, have to say there was no rust on any of the internals only the usual suspects sills, arch lips etc but nothing dramatic.
One thought I have had on the sills is to get powder coated and then painted to correct body colour, but then it would be better just to have them galv dipped and then prepped and painted
