The best touch-up paint I've found for matte/flat black:
http://www.amazon.com/Birchwood-Casey-Super-Black-Touch-Up/dp/B00JSAE0ZY?ie=UTF8&psc=1&redirect=true&ref_=oh_aui_detailpage_o01_s03
There's also a gloss black version. This paint pen has a chisel tip to allow for very precision...