Under Linux, my C++ application is using fork() and execv() to launch multiple instances of OpenOffice so as to view some powerpoint slide shows. This part works.
There is no good way. The only real options I see, are:
You could look around in the process's address space to find the connection information and window ID.
You could try to use netstat or lsof or ipcs to map the connections to the Xserver, and then (somehow! you'll need root at least) look at its connection info to find them.
When spawning an instance you can wait until another window is mapped, assume it's the right one, and `move on.