How do I save stock footage as flash file with transparent background?

Hi
I have some stock footage of smoke on a black background (.mov format) that I would like to convert to a flash file with a transparent background, which I will be overlaying over a PNG image on a webpage.
I have managed to remove the black background in After Effects using a plugin called UnMult, but when I try to render as a FLV file in AE, even though I check the option to preserve the alpha channel and encode using the On2 VP6 codec, I still get a black background.
So I am wondering what else to try, whether it be with AE or Flash CS4. Is there a way of achieving this effect by directly importing the MOV file into Flash CS4 and removing the black background there, or do I have to use AE, and if so, how to achieve the effect I am looking for?
I would be grateful for any help in getting this together
Thanks
Nick

You can put the video file in a movie clip and change it's
blending in the properties panel to multiply or screen.
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