I am not too sure where to start...

I have a computer with 4 monitors. The main application is set to be the topmost window and uses all four displays and the top two screens are grayed out. I have built a program to be the topmost so it sits on top of the main application on the top two screens but, the main program has child windows and popups that can go into those top two windows and I cant see them while my program is loaded. I've been at finding a solution for this for a week now....

How could I make my program hook into that applications frame and load my program inside its frame and move it to the top two monitors?
or
How could I make my program monitor when that application has a new child window or a new window opens, it moves it back to the bottom two screens?

Any help would be a lifesaver....

Thanks!!!