I think - might be wrong but I think - what you want is Shift Channels. And set the Take Alpha From to Blue channel.
This will make the video use the blue as an Alpha channel. Set that layer above your other footage and set that layer's Track Matte to Alpha.
Are you trying to use one layer's blue background, to cut out from another? If so, then it would be better to use Keylight to chromakeying out the background, and use the Track Matte to Alpha to sort the cutout.