Not sure about inkscape, but when I go to color stuff in photoshop, I usually start by putting the lined layer at the very top on multiply, then color on solid layers (no blending options or transparencies) below, starting with the areas that have large amounts of color (faces) to smaller details (eyes). If you're using inkscape you probably don't have access to photoshop, but I think gimp might be able to do blending layers. Not 100% on that though, since I've only used it a couple times.