I don't exactly understand what you mean, but you should start by building a custom video player which uses NetStream to play the video. You do not want to embed the video in the timeline. You need to keep the animation and the video separate from each other.
Using NetStream gives you a lot more power and control over the video, allowing you to do whatever you need to do with the animation part and have separate control over the video. And the animation can interact with the video and the video can interact with the animation. For a good starter tutorial on creating your own NetStream player:
http://www.gotoandlearn.com/index.php?currentpage=13
Start with video tut on page 14 and then progress to 13.
Best wishes,
Video Man