Charlie;
I'm no expert, only got my setup 10 days ago, so I'm in the learning stage. What I find works for me is as follows. Open a new layer, rename it "background", Select a brush ,something that is a bit wide. Select the background shade. Using a light pressure on the pen, shade in the background without regard for whether I'm going over the lines or not. After it is filled in, I select an eraser with a smaller size and go over everything erasing what I don't want. Hope this helps.
Cheers
Don