Unfortunately you cannot use RadWindow as application root, because the WPF doesn't recognize it as a Window and doesn't show it correctly.
Except this, you could use just like normal WPF window - inherit with XAML and add functionality and defaults in the new class and just use it from the other part of the application. You could use it in code behind and in XAML as well. We don't recommend placing RadWindow in XAML (if it is not the root tag), because in this case we need to remove it from the visual tree in order to show it correctly and this is not consider as a good thing. We've added this functionality to make it easier to customize with Blend for example.
If you want to add functionality you could use both of the approaches - inheritance and attached behavior. If you need to add functionality to all of the windows in your application I would suggest you to inherit from the RadWindow control and use the inherited class.
If you have further questions, don't hesitate to ask.
the Telerik team