GreatNate

I just did this recently, I used a Chroma Key for transparency, just layer it in Video Pad and use the Chroma Key Video Effect. On another project though, I needed to export it with a transparent background (a stinger transition) so I had to export it as an Image Sequence as PNG with Transparency, and a third party tool to turn that into file type and encoder that could handle actual transparency (WebM or mov) in video. Hope this helps.