Just paint over the lineout. Because it`s in another layer you won`t color it over. As you can see I already did some shading on the top of her head. Again use the ’freehand’ tool to select where you want to shade and click on: colors – adjust – brightness/contrast and adjust the brightness to -20 and the contrast to 0! (Photoshop equivilant Image > Adjustments > Brightness & Contrast). You`ll get a darker spot. I did this three times as you can see.
I use three ways to shade and highlight something, but that`s coming up later. Just enjoy the ride…
OK, the shade is too hard, so we`ve got to soften it up a little. I do this by using the smudge tool. Retouch tool – retouch mode – smudge. Play with the tool around a little bit so you`ll see what size, opacity, hardness, step and density you need 
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Don’t worry, practise makes perfect. Alright, I did some more shadows and i smudged everything. It looks like this…
