What I'm about to say doesn't have anything to do with Keyclone, but just for general info --

Darius said his main is "fullscreen." If this means "full screen mode" as in DirectX exclusive mode, then so far as I know, there's no way to do this.

But if he means the main is in a maximized window, then here's how a program could keep the small window on top while the main window has the focus using a Win32 function:

SetWindowPos ( hwndLittleWindow, HWND_TOPMOST, 0, 0, 0, 0, SWP_ASYNCWINDOWPOS | SWP_NOMOVE | SWP_NOSIZE );