Here's a bit of a walk through of the process I go through when coloring. I mostly use paint tool sai, the air brush with the selection brush. I use the multiply, screen and luminosity layer types. I typically do the flats then do the shadows, then add the high lights.
Link
billsc26
Thanks so much for posting this kind of in-progress picture. I think they are incredibly helpful for people who want to learn, or just people who are curious about how other artists do things. Thanks!