Adding flags with video editor

I have an animated chart that was created in flash that I would like to interact with. There will be a voiceover explanation of the chart and I wouldl ike the chart to animate on cue with the voiceover. I have the Suite so I have the editing programs, and I know that I can add flags in both the audio and flash files, but how do I get them to work toghether? Anyone with any guidance or explanation would be greatly appreciated!

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