I don’t know enough about grease pencil, but I’ve had my share of issues like that where things overlapped or one thing got in front of the other and the perspective was wrong, a total mess. I got various things resolved by watching Paul’s course, there was a nugget of info here and there and I was like oh, this would solve this problem. Here’s the link, perhaps watching it would do the same for you:
https://cgcookie.com/courses/panels-create-a-comic-book-with-grease-pencil-in-blender
Also his livestreams are full of great info.
https://cgcookie.com/live-streams
