I have two monitors on a MacBook. I mostly run with the lid closed and OS X doesn’t always use the correct monitor as my main display.
In the past I had to disconnect the external monitors and reboot, then connect the monitors in the correct order. Painful.
Recently, I discovered that the utility SwitchResX has a menu option to handle this.
Combined with the other features for setting quickly selecting resolution modes this is what works for me. I keep looking at the many of the other features and see possibilities for better workflows as well. But that will be another day.