How does the MacPro determine which monitor is primary

I'm aware of the display preferences settings and how the white bar controls which is the primary monitor. But it's strange how this is determined. For example, when I set up the computer, I initially only plugged in the Thunderbolt monitor and it was obviously the only and primary monitor. When I plugged in the 2nd monitor (Cinema Display), rather than that becoming the secondary monitor (shown on the right in the preference window) it switched to the primary monitor. I then had to rearrange the monitors in display preferences to get things correct. For most of what i do this is fine. However, if I shut down and restart, the start up screen starts on the 2nd monitor (as if it's primary) until I acknowledge a pop up dialog (something my work installed) and then the monitors switch back to how I have them setup. When I first set all this up, I had spaces off. I have since set most programs to the primary monitor, with only my email program on the 2nd monitor.

This morning when I tried playing music from iTunes, the sound came out of the 2nd monitor and not the primary.

So what I have been trying to figure out, is how to make the computer/OS always recognize the Thunderbolt monitor as primary. Also trying to understand why it wants to default to making the 2nd monitor the primary.

Hopefully this makes sense

I Know and have done that but it doesn't really answer or solve my question. For example I have the white menu bar on the Thunderbolt monitor but when I turn on sound it comes out of the 2nd monitor. Also even without moving the blue panels or the white menu bar what determines which monitor is the main and why can't I force the Thunderbolt to be the main without having to use the display preferemce window to "artificially" make it the prime. I believe when I first plugged in the monitors everything was more or less as it should be but then I had to move things and restart and the monitors flipped.

Is there a preferences file that I could remove and start again? Or does it matter which thunderbolt or display port the monitor cable is plugged in to? I have been using 2 displays for a while now and something is definitely not right. I can sort of work around it using the display preferences panel but something is off.

I figured this out on my own. I unplugged the second monitor, configured the single Thunderbolt monitor then did a shutdown and restart. Once back up and running, plugged in the second monitor. thunderbolt is now recognized as the primary monitor and sound and video are directed to that.