I don't know, but from what you are describing, it sounds just like you would just need alpha in your video and key that over your current video. From what I am used to working with as a travel matte, you have three files, not two. Two video files and one Matte, you set the matte to be a travel matte and tell which video file to replace which part of the matte. You can then move the matte around without affecting the video layers' scale rotation, etc.