Flyout menu that overlaps HTML

Trying to figure out if one can overlap a Flash menu with the HTML it is embedded into–like a DHTML or CSS menu. I would like to achieve the same effect as the menu at museum.stanford.edu which is done with some real complex and weighty JS. Also, is there any way to do this in Flash with the same functionality without having to load a new menu on each page?

Any clues or links to tutorials would be greatly appreciated.

Thanks,
Gazzer