There are a few different ways to CG. And each person probably does it a little differently.
1) You can also use the Layer options. What I do is have the first layer of colour I make be the lightest colours. Then I do two additional layers set to Multiply. And then just do the darker areas etc. Leaving the light base colours visible for highlights.
2) You can also do one layer of colour and use the Dodge and Burn tools for darkening and highlights.
3) Some people even use the Gradient tool instead to get the contrasts. By selecting areas with the Magic Wand tool or manually selecting with Polygonal Lasso then dragging the Gradient tool line across the area and letting go to get a gradual contrast from dark to light in that area.
4) If you're doing it like animated anime style cel shading then you might do a base colour layer and then use the polygonal lasso tool to draw out the darker or lighter areas so that they are straight and then fill them in with the darker shades or lighter shades. Then you can use the Blur tool to soften the edges if you like.
But there are probably other ways.
Oh yeah, when tracing the lineart you scan in do you use the Pen Tool or something else?
I just use the Channels method to isolate the lineart ( see here:
http://www.cs.nott.ac.uk/~dgf/tutorials/1lineart.htm ) works very well. Hmm but I seem to get small splotches that the Magic Wand picks up making white areas when I Fill. Might be traces of when I use the rubber to get rid of pencil lines after inking? Or maybe I'm not scanning at high enough resolution =\