Change audio output of Logic Pro 9 I have two Apple Cinema displays connected to my Mac Pro, System preferences sees both displays for audio output, however Logic is only sending audio out of my secondary display, not my main one, and there is only one Display Audio option in Logic settings.

More info:
if I unplug the secondary display's USB cable, and reset the Logic audio output, it goes to the main display. However, if I quit Logic and then reopen it it reverts audio output to the secondary display, along with sending my workspaces there.
From your question it is not clear if you still have a question, but let me give you a answer anyway.

There is nice little app on your Mac called Audio MIDI Setup (in the utility folder)

Open it and use the setup to for example have multiple audio output, or set up and Aggregate devices and so on to your desire.