sp,
Some recommend paint, some have great results with Sharpie type permanent markers and the "before or after" application seems to vary. I personally prefer Mr. Metal Color Stainless lacquer based paint done after the rigging is completed. (being careful to protect the model surface from drops or "flinches" of the brush!) Whichever medium or timing works for you I'd say, there doesn't appear to be a right or wrong method.
Cheers,
Lance