I think creating a website in Flash, is the same process you useto create animation. You create your basic page and on them you create Buttons and links that, when clicked upon will activate another animation. So basically, the whole website is a large interative animation which requires the user to click various links in order to see more.
You then export the flash movie into a web editor (dreamweaver, Net objects fusion etc)and embed it onto a blank page. You can then upload the webpage with the flash movie onto the web.
I'm not sure what I've said is accurate but I have used flash before for animation purposes and this is the way I think flash websites are made.