You can get touch-up paint in a little bottle with a brush built in to the cover. Jeep dealer can order it or may have it on hand. Good body shop supply or automotive parts store that deals in auto paints can also mix it up if you give them your paint code.
For getting the rust out of tiny chips, I used to have some liquid that a body man gave me, that essentially ate the rust, then you rinsed it off, and let it dry before touching it up. It was kind of nasty stuff. I've used a piece of fine sandpaper, folded and worked it carefully in the chip to get rust out too. Or gently scraped it out of a tiny chip with the pointed end of a small nail.
I like to pick up some automotive primer in a spray can, and spray a bit on a piece of cardboard, then dab the primer into the chip using the torn-off end of a paper match. For a miniscule chip, use the broken end of toothpick to dab paint in. Next, dab the touchup paint into the chip. Don't use the silly little brush, especially on these little chips. Again, use the paper matches. You can lay paint right into a chip with that torn off end. Body man taught me this. Keep adding thin coats, letting each coat dry well, until the surface matches the surrounding paint after it has dried. It can even be a bit high. If it is, or if it looks a tad rough, you can easily do a little buffing to get it to blend in nicely. I use a product called Wizards Turbo Cut. It is a super-fine rubbing compound which is also very handy for buffing out scratches in paint. And it can be buffed by hand with a soft cotton rag, very safely. This product can be used on new paint too, so it works well for the touchups.
I've made a lot of little chips nearly disappear doing the above. Best of luck.