Character Animator & Video Workflow

I understand that only stills can be used as backgrounds in Character Animator.  However, I have a motion graphic video that I want to Puppet to interact with / point to items on screen.  What would be the best workflow for timing for this?  Currently it's a two person process where we start the video and the animating at the same time and one person animates the puppet whenever the video person says to.  Is there a better way to do this?