I also use Sharpies and Bic Mark-Its to color my pearls and rhinestones. I have a lot of clear rhinestones that aren't sticky on the back so to color them I place them on the sticky strip of a Post A Note and color away. This idea is not original with me but it doea the trick.
Also, since I have so many clear rhinestones I used some to make a color chart showing the end color of each of my markers. That way I can find the exact color I need.
If The Glue Sticks…Embellish