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I have removed the sills and painted the steelwork. Do they rust from the inside too as I have only painted the outer surfaces?

Frankly the only safe assumption regarding rust is yes it can sprout anywhere that water and/air can penetrate. You don't say what you used to paint the exterior but some suppliers of rust treatments use spray cans the have a flexible tube and spray head to help cover internal services that have limited access.

The rust wil be coming through from inside so, if you don't have it breaking through at the moment, the best thing to do would be to get some wax rust protection such as Dinitrol or Waxoil in there sharpish! An aerosol will give you noting more than a temporary warm feeling. Get in there with a proper compressed-air driven wax injection kit which will blast the wax into all the nooks and crannies.

Thanks guys - the compressed air system sounds ideal. Is that professional equipment that a garage may have or can I purchase a hand pump type?

Outlets such as Halfords stock DIY rust prevention fluid in a can with a screw on pump on the top. Off the can comes a length of tube and various application nozzles.

This stuff gets everywhere during application. Sheet out the ground with polysheet or you will later be treading it into the house. Make sure you remove the seat belt reels from the car and stuff rag in their place. Removal of the belt reels ensures you will not get the wax oil all over the belts when you use the equipment!

Mike