Usually video and audio are encoded separately. Then you have to join both of them to make a movie that you can play (you can of course play audio and video separately in two players but to get synch would be rather hard). During multiplexing the audio and video track are combined to one audio/video stream. The audio and video stream will be like woven together and navigational information will be added so that the player can example fast forward/backward and still retain synch audio/video.
