The latter, mostly. Since it is comic art and most of the black lines vary greatly in thickness, I started with a black outline of a majority of the image and have been adding color areas on top. I figured that with this type of art, this method would be the easiest and most effective.
Separation of my two main layers attached as an example.
EDIT BTW Within the black layer, I have separate black backgrounds for Spiff and the Spaceship, so Spiff may be used separately in something else if needed.