Both 3D and 2D animation have their strengths. 3D offers a more solid sense of space and grounded environments. 2D Animation has the capacity to be much more expressive, free-flowing and organic. Bridging the two can lead to some interesting shots.
Freelance Animator and Illustrator, Howard Wimshurst demonstrates the methods he uses to draw 2D animation overtop of 3D animation using Flash (Adobe Animator) and After Effects.
The process involves brining a 3D rendered sequence into Flash, drawing the animation over top of that sequence, and then exporting the necessary layers so that you can composite them in After Effects.
If you like in-depth tutorials on animation, like this one, Howard Wimshurst’s animatorguild.com has a lot more. The site has quite a bit of lessons and resources that you can go through.