IIRC, I've seen at least ten different methods—experiment and find what works best for you. There is no one "best" way, IMVHO.
On my latest, I tried at least four: washes, pencil (colored and graphite), ink, and dry brushing. Washes work for both recessed and raised lines, pencil and ink can be made to work for both, dry brushing is usually limited to raised detail. The hardest (for me) is spraying a darker or lighter color on the panel lines, then overcoating and sanding. I've seen some great results, but it has never worked for me.
That's part of the fun—trying new techniques!