Combining Live Action with Animation (workflow)

Hey guys,
I’d like to make my first short film that combines live view and animation elements (like in Space Jam or Who Framed Roger Rabbit), but the problem is I don’t know how the workflow should be set, so that production goes the best it can go.

Let’s say I have a SHAKY video of some building and I’d like to animate King Kong climbing up on it. Should I import that shaky video in Toon Boom Harmony and just frame-by-frame draw King Kong directly on the video? Or should use some tools to do that? What do you recommend to get through that shakiness?

Thank you for your advice!

The workflow would probably be to remove the shake from the footage, you can do this in adobe after effects (or other software) with a single or dual point track. (single point if there is no frame rotation at all, dual if you need to track position, rotation and scale for that matter).
When you are working on stabilized footage you can onionskin the animation more easily, you can always reverse the stabilization process later to apply the inverted motion to the camera+overlaid animation to achieve a more natural hard held camera look.