I don't have info on how to paint them--but I want to ask how important you feel they are, and if you could live without them.
My running boards faded first, then shortly thereafter began rusting, badly. Not too long ago I simply took them off and tossed them--and the truck instantly looked about five years newer.
If you really like the look of the boards, or have physical needs for them (disability, young kids, pets, etc.), then yes, by all means, pursue painting or replacement. (If you go for painting, check them over for rust, inside and out, to make sure they're still in good enough shape for the paint job to be worth it.) But if you're not using them regularly, and don't mind the board-free look, I definitely recommend that you consider sending them to the scrap heap.