I have the Delmonico Red pen and it works perfectly. You have 2 choices.
1) Follow the instructions on the pen. You dig out any impurities using the hard tip supplied. Then you add some paint from the paint end. Let it dry and then come back over the top with the supplied clear. It won't be perfect but it will hide the defect. It'll be a little rough around the edges.
2) Clean up the area really well and hit it with a cleaner/degreaser. Fill in with paint, let dry. Repeat until you have the chip built up where it's only slightly below surface. Then fill with clear and wipe smooth. Let dry. Come back later and clear again so that you are slighly above surface. You are wanting to build up a little mound that you can sand down. And I do mean little. Let dry for a couple days in the sun or just drive it around as normal. It'll cure. Come back and wet sand starting at maybe 600 grit and ending at 1500 or more. Then polish. You'll have completely restored the paint without a single trace of damage. Make sure to try to focus the wet sanding just on the new clear coat and only hit the original clear minimally to blend. The clear on these new cars is super thin. I've sanded thru it before in the past and had to have a section re-cleared to repair my mistake. Live and learn.
#1 I do for almost all minor dings.
#2 I save for something more substantial. I'd say once the ding is the size of a BB or bigger. I don't get these often and haven't had one this size on my current truck yet, thankfully. But I've done this method many times in the past and it always comes out looking perfect.
Scratches are entirely different. If you've gone down below the clearcoat with scratches, to the point you need paint touch up, this is going to do nothing more than cover up the metal / base coat. It'll still look pretty bad but it might take away enough of the scratch to not draw attention. Circular dings / nicks is where these pens really shine. Scratches, not so much. You can attempt #2 on a scratch if the paint isn't metallic. If it's metallic, which most of our paints are, it's really hard to get it looking good. The flakes don't line up and the line will be inconsistent. Usually will come out lighter or darker. Just depends on how close the paint pen matches up.
Metallic paints, in general, are very difficult to touch up once you go beyond a ding.
Oh, and one final note. There's absolutely nothing you can do with these pens that can't be undone. If you apply the paint and you don't like it, just use a little bit of paint cleaner/degreaser and wipe it right off and start over. You may have to polish a little afterwards as the chemical can haze the clearcoat a little.