I had posted a question about using CineGobs to generate transparent background videos for imovie, but did not receive any good answers, so after learning how, I wanted to post for others. I am a mac user but have boot camp and have windows on my mac. These steps will be abbreviated and you may use other ways but this works for me.

Only use AVI and PNG formats with Cinegobs but when you are finished you have to convert back to a mov file for imovie. Input your video, and I use AVI that I have converted from another file format if not AVI. Set image input to "RGB + Alpha" and output to "PNG Single File". Do your thing with the video. Make sure that you use a separate folder for your outputs, since it may get large and it is easy to discard. Render the video. As a note, when you look at the inspector for a video file it has to have colors of "millions +", if the + is not present it will not have a transparent background. Use software that will let you "open image sequence" and then "Save", I use Quick Time pro for this.

If you use AVI single file as the output, it will have the million+ designation, transparent background, but I could not find a way to convert to mov and retain the transparent background.

I hope this helps someone, it took me a lot of trial and error but could not any good tutorials or help for my question.