Question from the blog: Under paintng and under drawing settings

Recently received a question on the blog and I had the opportunity to answer it sooner rather then later. William asks..."What method (how do you) set up your line drawing so that you can color "under" it, coloring so that the lines are not covered up, if that makes any sense. I see underdrawings used all the time by artist in Imagine FX, but NO ONE describes what settings, masks, layers