Transparent Video Background and Layering Videos - Help!?

I was wondering if it was possible to import a video with a transparent background into Storyline and then being able to place it on top of another video/picture and both playing simultaneously. My idea is to have an animated character than I can use on slides/interactions and it can just pop in. However, when I import videos there is a big black box despite the video being transparent pre-import.

I have spoke to support and they have explained that due to flash now not being supported the old method of FLV file is not working and so this can't be done.

Does anyone know of a work around, or a different way I could achieve this? Any help, guidance, or advice would be greatly appreciated! 

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