Craig,
I tend to break my applications into several user controls for the
layout of the application, i.e., menu, toolbars, login prompts, etc.
For the body of the application, I tend to place those in a single user
control for ease of use. For example, if you want to change the entire
design of the interface, you can simply drag and drop the content user
controls within the designated area.
I don't think there is any documented best practices for user
controls, simply whatever you feel would make your life easier.
Aaron