the brush that comes on touch up paint is crap. my way of touching up is...
1. get any wax off teh paint in the immediate area.
2. put one thick layer on to try and full in the scratch and then wipe it over with my finger to get the paint off the non scratched area (a paper towel will just soak up any pain that is in the scratch) the trick is to get all the touch up paint in the scratch and not on the sourrounding paint.
3. the first coat of paint should pretty much fill the scratch, after that just put a few small thin coats so that it looks ever so slightly raised from the rest of the paint. (it will dry looking even)
4. after the scratch is filled in to your liking, let it dry for a full 24 hours and then use some rubbing compound/polish and gently rub the area with it so that it blends with the rest of the paint.
5. when finished, put some wax over it to protect the paint.
some people have different ways of doing it, but this is mine and it comes out to my approval (and i have nighthawk black pearl). good luck