Back in the 'old days' you could just specify which X11 display you wanted to open your window on ...
That would be for the default first screen typically.
Then you could run your windowed apps from the serial console/remote shell and they'd pop up on the desired display. Modern linux seams to have more layers of security, but on the gumstix everything runs as root so this would be the first thing I'd try. (Disclaimer: I only have headless gumstix's running here now so I can't give this a quick try myself and then not post this if it doesn't work.) :-)