All right, you should be able to color on the color layer and it won't affect your lineart. Now, go to Image<Mode<RGB Color, and click "Don't Flatten" when the screen comes up (Flattening merges all your layers). This changes the mode from the Grayscale that we scanned the image at. While on the Color Layer, use the Polygon Lasso Tool to select the first area you want to color, keeping the selection line INSIDE the lines of the lineart. Then fill the selected area with the base color of your choice (something between the shading color and the highlight color you want) In this case I selected the face, because I feel it is a good place to start. It is outlined in red to better show you the path. Next to it is the image with the lineart layer turned off, this better illustrates that you are not affecting the lineart layer, and that if you deselect the face region, it is easy to reselect it using the Magic wand with the tolerance set to 1.
Now I've selected the area of the face I want to shade with the the darkest shading. and I create a new layer and name it faceshade, then with that same selection, I fill with the shade color on the new layer. Remember to keep lightsourcing in mind, for this picture, the light is coming from the top right-hand corner. Also, you can highlight multiple areas with the pollygon lasso tool by holding down shift.
Now I create another layer between the color layer and the Face shadow layer, and I call it "faceshadow2" I then use the airbrush tool with the pressure set around 30% and the brush size at 65 and I airbrush in multiple layers of shading to create a soft gradiated color. Your layers should look something like the image below.
Next, make sure you have the Faceshadow layer selected and go to Filter<Blur<Gaussian Blur. This blends in the dark shading around the edges of the face. I set the Gausian Blur to 7.3 pixels, but set it to your preference. Also add in some highlights with the airbrush and a very light skin tone on the "color" layer. This representation is a quick job and you can add any level of detail you wish.
Fill in the rest of the skin (i.e. neck ears arms ect.) using the same process descibed above, remembering to make new layers for each piece. Next we go to the color layer and select the white of the eyes area and delete the skin color from it.
