Panel lines

Regular pencil tends to have a bit of a shine...so ideally the Dullcote should come after.

This also limits the likelihood of mucking up your flat coat through the inevitable handling that happens while drawing on the panel lines.

  It might be helpful if you post a photo of the real aircraft you're building and pick our brains on how we would accent the panel lines. Just a suggestion.

Raised or engraved panel lines?

The only thing to really worry about is making sure you clear coat the pencil lines or you can accidentally smudge them. 

I will suggest doing one section at a time between clear coats. Basically save your work before moving on from the fuselage to the wing and such.

Depends on color.  Panel lines are not that noticable on dark paint.

Even on light colored paint it is easy to overdo these lines.  Less is more is the old mantra.