I would recommend you to define RadWindows in separate files. You could also define them directly in the page with the GridView control, but it would better to move the RadWindow controls out of it and separate the xaml and code-behind of the windows.
I would recommend you to inherit the RadWindow control in XAML (like you do with the UserControl when you are using the VS template "Create new UserControl"). You can do this by creating a new UserControl. After that you should change the UserControl tag in the XAML file with telerikNavigation:RadWindow and change the new UserControl to not inherit from UserControl, but from RadWindow. I've prepared a small example that demonstrates the idea.
the Telerik team