Okay, I'm gonna attach you an image, use it along with the guide I'm gonna post below for coloring, or at leats, the method I use.
http://img8.imageshack.us/img8/5660/coloringn.jpg
Once you had finished the lineart, create a new layer below the lineart layer and color the areas of your drawing with solid colors, using the lineart as guide for spaces, you can always use the
polygonal lasso tool to help yourself.
(1) Now, once you have your color layer ready, create a new layer below it and fill the color area with
50% gray. (NOTE, by 50% gray I mean the gray coloration on the color scale, not opacity).
(2) Now, set the color layer as
Overlay, by having a 50% gray below yur color layer, the colors will not be afected by setting their layer as Overlay. So if your color is orange, it'll still be orange, if it's blue, it'll still be blue, etc...
(3) Now, on your layer with the gray color using the
Burn Tool you're gonna add shadows, and with the
dodge tool you're gonna work lights. These two tools work as brushes so you'll have no problem using them. Add all the shading & lighting efects on the gray color layer (At the images I've hided the color layer to show you)
(4) Now, if I visualise the color layer it'll look like this
(5). In these cases, you may use the
magic wandda tool (with tolerance of 0) to select especific color areas on your color layer and with the section selected, return to the gray layer to work the efects. By having color layer and efects layer separated, you're free to change the color of your drawing anytime and you're protecting the color layer in case of making a mistake on the shading/lighting process, hope it was usefull.