When you're messing with video files, you first demultiplex ("demux") the file into separate picture and audio streams. Then, once you've got the elements the way you want them, you remultiplex ("remux") the separate streams back into a single video file with synchronized picture and sound.
Just wanted to chime in and voice my admiration for how you've brought the communal experience of the cinema to home theater, which can be a pretty solitary pursuit. And the effort you and your family put into programming for your theater really shows.