I have a stone chip above the blade-shaped GTD badge on the wing. It has only taken the top colour coat off and it is absolutely tiny, but I am shocked how thin the colour coat is.
Halfords do a kit with lots of rubbing pads that help rub down.
I always used to use a model brush with a very fine tip (or maybe even a slightly sharpened matchstick on a tiny chip) and make a small pool of paint diluted with a tiny amount of ethanol to get the thin layers on rather than a splodged thick siingle layer that needs rubbing down. Easier to do with the solid colours - it's too easy for the metallic/mica particles to fall out of solution on thinned metallic/pearl paint.
If you do have to do a thick splodge with the base colour then I would leave it to harden a few days and shrink back as the solvents evaporate. Then i'd be rubbing it down with one of those abrasive pads from the Halfords set until it is noticably lower than the surrounding paint. Clean up the rubbings with some water and dry off, then apply the top lacquer layer. Another few days to harden and then lightly rub down the lacquer layer flush with a very mildly abrasive polish like Mer.
I'm no pro, but I get decent results on stonechips doing it my way. Someone probably has a better (and quicker) way of doing it to a good standard.