I than duplicate the background drawing in another layer and set the blending option to multiply (I think... ) All the colour work is sandwiched between the two layers. This method keeps the colour beneath the linework, so that nothing gets lost beneath the colouring. It's like having two layers of clear paper and the line drawing is sitting on top of the colours, if that makes sense. (I use a lot more than two layers but you get the idea) Each layer of colour is set to a different opacity, I'm going for a slightly washed out look, not overly intense but with moments of richness. This process is just an extension of my traditional work so the learning curve has been pretty gentle.
And if you're wondering this is a bit of an homage to Maurice Sendak.