I have seen those Dupli-color brand touch up pens in stores for quite a while. If you are going to use the paint, that if fine. However, do not use the brush or the roller ball piece. I'll do a small quick write up on how to properly do this.
1. Examine the scratch. If there are loose pieces of paint or jagged edges on the scratch, remove them.
2. Wipe down the scratch and the area with IPA/water 50/50.
3. (Some people dont do this, but I will also get one of the duplicolor pen with the filler/primer.) Use the filler/primer, and a very fine painters brush to put one coat of filler/primer in the basin of the scratch. Allow this do dry approx. 15 minutes.
4. Using a clean, very fine painters brush, apply a thin coat of the paint to the basin of the scratch. Do not use a blob of paint. It is better to do ten thin coats than one big one.
5. Repeat # 4 until the paint is brought up just slightly over the surface, allowing dry time for the coats.
6. Utilizing 2000 grit sandpaper, sand down the surface to nearly flush with the rest of the area.
7. Using a rotary type (Dewalt, Makita, Clyclo, Flex etc.) compound the area. Use a finishing polish to bring back maximum gloss.
8. Apply a sealant or wax of your choice.
Side note: This may be a good time to go ahead and have the entire vehicle polished. If you are not up to the task, locate an experienced detailer. I think I know of a couple.