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It sounds as if you connected your UI element to the File's Owner object, which is an instance of NSApplication.
If you haven't done so already, you want to drag a NSObject out of the Object Library palette in Xcode 4 to the margin to the left of your layout. Once you've done that, and have selected it, choose the identity inspector and, in the Class field, enter "WindowController".
Now that you've got a representation of your WindowController, which as you said contains startServer:, then you can connect your UI element to that. Be sure your startServer method is of the form:
- (IBAction)startServer:(id)sender
or you won't be able to make the connection.
Good luck to you in your endeavors.