Animated website structure question [example inside]


I´ve been practising in the development of an animated flash website, and I was wondering a few things about way the website should be structured.
The website will have alot of animations to- and from pages. I have no idea how to structure this in the fla, the way I do it creates alot of mess on the timeline because of all the page transition tweens. I can see this creating alot of problems with coding.
I know I could use actionscript for the animation, but I was hoping that there is a good way to do it manualy aswell.

This website is quite similiar to what I want to achieve.

My own design is available to view here:

the pages are blank because I didn’t want to proceed the design till I solved this.
The purple building and the upper right cloud are links to example pages.

Thanks in advance.