This function cannot associate a hot key with a window created by another thread.
The sentence that I copy pasted from the page about "RegisterHotKey()" http://msdn.microsoft.com/en-us/library/ms646309(VS.85).aspx makes me think that in order to do what you are trying you either need to inject this in to the target process (DLL injection feels like the right way to go here) or you need to write a launcher for the target process with this function included in it. Does anyone have more input on this? It's not something I've tried myself before.