I do something similar...I draw the lineart and some of the shading on paper, then scan it in, adjust the levels, desaturate it and then make it transparent by eliminating the whitespace and turning on "preserve transparency" or "lock transparent pixels." I then add the color in a layer underneath the pencil layer, then I have two layers above the color layer, one set to "multiply" for shading, and one set to "color dodge" for highlights. I may also add textures in other layers set to "overlay" or "soft light" as well, but I mostly just use that for weapon design.