If the SWF is embedded in an HTML page (or better yet a PHP page) then they would "talk" a lot better. Javascript or PHP would enable varibles to be passed to the movie, Javascript would mean that the end user would have to have both Flash and Javascript to navigate, this will turn some users away. PHP would be server side, so they'd only need flash, but the page with the swf would have to reload to get the uploaded varibles (which could mean reloading the movie if the users cache was cleared, or the movie wasn't cahced).
Two other alternitives:
1: Dump Flash. Up swing - is that more people can veiw your content and navigation. Downshot - you lose interactive animation (unless you use gifs).
2: Add a flash button (flash can talk to flash). Upshot - cool animated button. Downshot - flash navigation makes site more forbodding by people without flash.