Blacken the scratch, wait about 15 seconds, then rub on the mark with your thumb.
If you just touch the Sharpie to the black, it will be a little shiny (unless you want it shiny) and obvious.
If you wait a few seconds, then rub on it, the rubbing will take away the shine without removing the black from the scratch, and leave a dull surface. Looks much more natural.
Mike