I was doing this before with Gimp.
I was bringing screen shots of the frames most important to the animation to Gimp, then drawing on a separate layer over them. Once done then import just the drawing to Blender in the VSE where I had the video, and just match the drawings to the video. It works. But it would be lovely to do the drawings directly in Blender with its new Grease Pencil. I just don’t know how to do them over the video.
This amazing video shows how to use Natron to composite them. That’s cool and all, but if I could do it all in Blender then that won’t be necessary