For example, this is a pencil sketch (a real sketch scanned in ) over a background watercolour layer.

Name:  Tree frog pencil.jpg
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Size:  40.1 KBClick image for larger version. 

Name:	Tree frog pencil close.jpg 
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Size:	86.0 KB 
ID:	93346

I created a stencil for the frog shape to mask it while I painted the background and then inverted it to paint the frog. The pencil lines just sit on a layer over the top, and I used various amounts of Thinner to get the different opacities.