background-knowledge:
adobe media encoder (and all other DVD-asset-encoder), creating so called elementary stream, that means audio and video are seperated.
within your authoring-process you can put more than one video or audio into your timeline (at one time).
that´s necessary to have different audio-tracks for multi-language DVD/BDs or maybe different cam-angles as a mixed/multi-angle DVD.
so you need to have elementary streams before authoring to multiplex them again, to get all this working.
cheers
danny