Timeline question

Hello,
I currently have a Flash project I’m working on for school, a quiz like interface. I’m going to have boxes jump and morph around into other sections. But I’m not sure how to go about it. I found this site which has similar traits to what I’m planning on doing. I know it’s a lot of shape tweening, but not sure how to organize it along a timeline or if that’s what to do at all.
http://www.phillennium.com/home5b.htm

BTW, it’s a neat flash site.
THanks