I usually use three layers for both light and shadow, as you've probably noticed with your shadows here, they become a lot deeper :)
and then you need to make sure you're using the right colour on the right layer otherwise things look a bit funny but you'll probably be the only one to notice XD
If you start adding light layers you may have to make your lines a bit stronger to compensate, or you might be fine, have you tried playing around with that?
Unfortunately I cannot make thick lines, since I only use the mouse and as you may have noticed, my drawings are always like that. They don't have variable lines, let's say. But it is a great observation that you have made thanks.