I have a document based app in cocoa with three xibs for different toolbox windows. At app launch I would like the toolboxes to be visible very similar to Adobe Illustrator where the toolboxes are visible on either side. To do this would I need to implement my own NSApplication?
No, when the document spawns, in its controller class (or the app delegate, dependent on who owns the toolbox windows) call makeKeyAndOrderFront: on each of the windows that you want to bring forward.