I want to try Lightworks.  I'll probably use it on my next film. I don't have the answer to your question, but just try layering a png on top of your video in there and see what happens, I suppose.  It's a pretty basic piece of functionality so I suspect it would support that.

Incidentally, for this same upcoming film, for which characters will probably be computer animated, I'm planning on painting all of the environments in Photoshop. So, it'll be like matte paintings through the entire film.  Not unlike most 2D cartoons.  Should be an interesting way of working, I think.