At work, I have access to many appliances ranging from DataPower to Cisco to F5 and so on. Each of the user interfaces for configuration seem to have a different layout where on some the navigation is on the side while on others it is on the top.
How do usability guidelines vary based on whether something is a user website vs something that needs to be configured?
Either is fine, and both work well - it depends on whether the method you choose is implemented well. For example: most routers have a menu on the left-hand-side, and everyone uses these screens with minimal hassle. Conversely, windows options dialogs always use tabs (across the top), and no one seems to have problems there.
Even microsoft change their styles - properties windows in Visual Studio and the options windows in MS Word 2007 both have menus on the left.
It's personal preference, though tabs seem to work best with fewer options, and left-hand navigation is better for more options. That's probably the rule of thumb, if anything.