Hi Malcolm, thanks for your comments and question.
What I aim for with Animation Paper, when designing it, is to have it be very close to traditional analogue animation in the way you as an animator think and work. However, in the way you would do it cleverly today with modern digital features and conveniences.
Normal workflow in Animation Paper is to do rough animation, clean up and inking all digitally within Animation Paper. It is totally possible to import scanned or photographed backgrounds or animation, but doing the final clean up in Animation Paper is recommended before coloring.
In the current pre-release (Alpha 7), there are no coloring or paint features implemented just yet. These are of course planned and on our todo at a very high priority.
Let me know if you want me to go into more detail or if you have additional questions.