I used to use a black technical pen set (Koi-noor or Rotring drafting pens) which gave me a wide range of line widths to choose from. I used permanent waterproof ink and always gave it a day or so to dry before hitting it with any dull or gloss finish coats.
I used them to run ink lines down panel joints and to fill in things like windows.
If you do use a pen, test it first by applying the ink to some sprues, let it dry. then rub them, if if smears easily its the wrong kind of ink for permanent application. If its sticks good, then add a dullcoat or a glosscoat over it, if the clear-coating causes it to smear or run, better on a scrap piece then on your finish model. If when it dries, it takes and doesnt smear...your in business!
Good luck