Over the last decade Microsoft has put a great deal of energy into these sort of problems. Consider PowerToys and things like FancyZones.
Screen Switcher is an application using Windows Forms in C# that makes changing the monitor placement of a stubborn program simple.
After running into problems with managing programs on my multi-monitor setup, I wrote a basic program to make managing the monitor placement of the programs easier.
WMIC C# WinForms