You can see the order that the monitors will be searched in by looking at the numbers on each monitor icon in the monitors control panel. The first monitor is always one connected to the built-in video. If that monitor matches the settings your application wants, that's what it's going to run on. It would probably be a bad idea to try to change this by hacking the code that looks for a "good" monitor, as you never know what kinds of monitors your end-user has attached.
While you are working in AMT/PE under MPW, you may be able to take advantage of
the fact that MPW runs on the monitor with the menu bar. So you could open the
Monitors Control panel in your System folder, drag the menu bar over to a
different monitor and reboot. That way, MPW will at least run on a different
monitor than the one your application chooses to run on.