I'm still figuring out what software can achieve my aims.
The video is an instructional video where the person says, e.g. we are going to build a first box and a second box. How easy is it to sync FCP and Apple Motion, so that when the person says "first box", the animation of a first box appears, and when he says "second box", a second box appears?
This is just an example. My diagrams are far more complex than can be handled by FCP's simple shapes options. e.g. FCP seems to have trouble drawing simple lines, from what I've searched, let alone free-hand squiggles.