I'm still learning as I go myself but from what I have learnt so far is that it is much easier to color in the same layer as the line art. Unlike Photoshop you don't need to go in separate layers to color/shade/highlight etc this can all be done in the one layer/symbol.
If your using the brush tool to paint/draw then you might want to use the pencil tool to make the outlines for shadow/highlights because at the end, you can highlight the entire frame and remove the pencil by changing its color to nothing (the box with the red line through it) this removes the pencil lines and keeps all the shading and highlights you've put in.