I can speak to this personally. About 2 months ago, give or take, I did a repair of a keyed scratch on my 2010 Fusion, and at the same time filled in a few larger chips, plus a few smaller ones, and I used the Ford touch-up paint to do it.
Yes, the little bottle does come with a 'pen' applicator, and also has a little built in brush inside, that I felt looks like a nail polish brush.. but if you want it to look good, you won't use either.
The trick is to put the paint on the car almost like you're "tattooing" the car. In my case, I went to the local Michael's hobby supply store, and bought a super-fine paint brush, with a tip that looks kind of like this:
I then went over all the spots that I knew I would be applying the paint with an IPA solution and some microfiber cloths.. multiple times. This is to make sure that your little holes do not have any wax or other contaminants in them.
Then, I took the cap of an empty water bottle - the smallest one I could find - rinsed it out thoroughly, then blew it dry with my compressor. Finally, when I was ready, I shook the touch up bottle thoroughly, then using the brush supplied in the touch-up bottle, I transferred some of the paint into the water bottle cap.
Applying the paint is the tricky part. You just dab the tip of your super-fine paintbrush (like the image above) into the paint, so you just get a tiny little blob on the tip. Then you very carefully just poke the tip into the chip, scratch, nick, etc.. and let the paint ...flow.. into the gap. Remember, you're just 'tattooing' the spot. If you do it right, you will see the paint slowly move into the chip. Don't put too much in, but if you get it just right, you'll get a TINY little bit of a 'dome' on the paint.
Now... just leave that spot alone and move on to another. After a while, the paint will dry, and you'll see what was once a 'dome' is now shrunken into the chip. That's okay - you want this. Let it dry for at least 10-15 minutes... and then do it a 2nd time. Do it as many times as needed, using a little less paint each time, until it dries just SLIGHTLY above the existing paint. Then you're done applying the paint.
Your next step is to level it back down. If you can find a good leveling solution, then go with that.. as it will actually allow you to get the paint just slightly below the existing paint.. If you can't get that, then do what I did and sand it VERY CAREFULLY using some super fine grit wet sanding paper (2000 grit or higher).. and the move on to polishing/waxing.