Can I change which external monitor is considered the "secondary" monitor? I've got a MacBook Pro, and two Thunderbolt displays. I'd like to be able to change the brightness on them individually, like so:

For the MacBook, I'd use the F1/F2 keys on its keyboard.
For the first Thunderbolt Display, I'd use the F1/F2 keys on my USB keyboard.
For the second Thunderbolt Display, I'd use CTRL+F1/CTRL+F2 on my USB keyboard, as outlined in this AskDifferent answer.

However: the CTRL+F1/CTRL+F2 keys on my USB keyboard currently map to my MacBook's brightness - so now I've got two ways to change my MacBook's brightness, and zero ways to change my secondary Thunderbolt display.

Is there a way to re-map the CTRL+F1/CTRL/F2 commands, so they control the secondary Thunderbolt display?
I don't know how this applies to the mapping. But you can define what is your primary monitor by going to display prederencey and moveing the little menu bar to the display of choice