If you want to put alpha channel into a Quicktime video, one way to do is set the video codec to animation codec. After save the video file, you should play the video once by Quicktime, so that converted Quicktime can be saved.
The converted Quicktime file should hold the alpha channel. But how can you check it? A bother way to do it is compositing it with another video or image, and see if the alpha part can overlay the other. That’s what I did a few times.
But I found a easier way to do. When you are using Mac, the Finder’s quick look function can play a video quickly without external video player.
The quick look player do render alpha channel, I mean, if you play the quick look player, the alpha area of the video is transparent. So, you’ll see an icons on the Finder under the area through the video, as the image below.