I use photoshop, in the layers panel there are 4 buttons near the top of the panel you can use to lock the layer, the first button locks the artwork on it so that if you paint over it, it will only paint on the areas that are there.
That is what i used to color the linework (it's really useful for lots of things)
That is what i used to color the linework (it's really useful for lots of things)