Controlling Flash with Javascript

I have recently designed a site for a client which has not yet launched commercially. The layout involves two frames: a navigation frame (top) and a content frame (bottom). The flash movie resides in the top navigation frame and displays buttons that allow the user to access the five major sections of the site. When the user selects a button in the navigation movie, the content frame loads the appropriate page while the movie goes to and plays the approriate frames to introduce that section of the site. This process works flawlessly and creates a very nice user interface. Because I want the site properly indexed by the major search engines, all five links contained within the flash menu can also be found at the bottom of each content page. However, if the user selects the links at the bottom of the content page instead of form within the navigation movie, the content frame changes, but the flash movie remains unchanged. This causes the navigation movie to display incorrectly according to the current content area.
This is my first go round with this type of flash/javascript interaction. I have tried the behaviors window in Dreamweaver, but the available options don't provide what I am looking for.
Any help would be greatly appreciated!
Thanks.