I hate pens, and I do paint touch up 10-15 times a week, lol. My process (might be long but works well):
-take 2000 grit sand paper, punch a hole in it with a hole puncher. Now take that little circle that was left over, and a pencil/pen. Using the beck of your pencil, sand the chip down a little bit.
-the paint chip is now prepped
-Get a BOTTLE of touch up paint. Get a tooth pick
-dip your tooth pick into the bottle, and place the tooth pick that has paint only on the tip inside the chip, let gravity pull the paint down into the chip (best way to get a nice uniform and flat fill)
-waiting 15 min between coats, put enough paint on that your chip is actually overfilled and you have a "bubble" of dried paint that is above your paint of the surrounding area.
-get some 2000 paper again, and soak it in water for 15 min
-wet sand the "bubbles" flat, so they are even with the surrounding paint.
-buff out the scratch marks
keep in mind darker color will hide this much better then lighter colors