Ah that makes sense, have advised me to use pen... Then again people sometimes people suggest I colour over graphite :S Which I've seen people do, but sounds very smudgy. I do try building up the darker areas as much as I can, another artist advises good highlights being as important as good shading.
I also do that sometimes, but to avoid the linework to be totally smudged I usually start the coloring before all the major details in my artwork is finished (I add details after the colors are dry usually with black ink pens). But don't worry, it's great to experiment with various tools and techniques. There is no right and wrong when it comes to art
That kinda reminds me of watercolor a little, you start from the lighter colours to the darkest, I usually add outlines when the the color is all dried. Kinda find I layer it all the way to the outline.