Where can I change the window my app uses from UIWindow to my own subclass "MyWindow" with storyboard?
When using storyboards the application delegate and main window are no longer represented in Interface Builder. Instead, when your app starts, your app delegate is queried for a property called 'window'. If this returns nil then a default window of type UIWindow is created for you. To change this behaviour you need to implement a 'window' getter method in your app delegate that returns your 'MyWindow' subclass. See the documentation.