OK i found it after a little more web searching and thought I would update.
If you select your Mpeg flavor and a Aiff/Dolby. Double click on the Mpeg file in the batch window.
The inspector window should open up. In the inspector window click on the Extras taba and on the bottom it says…
“Multipexed MPEG 1/Layer 2 Audio”
Check the box.
Life just got easier.