Hey Phil,
If your app is installed in a user-level folder (e.g. %appdata%, the Desktop, etc.) or if your app is installed in a system-level directory (e.g. c:\Program Files\ZYX) and all your customers are running as elevated administrator users then you can do a completely "silent" update. That is wyUpdate still shows the progress as updates are being installed, but the customer does not need to interact with it.
If that's the case then you can use either the AutomaticUpdater (AutomaticUpdater tutorial for Windows Forms) or wyUpdate (see: http://wyday.com/wybuild/help/silent-checking.php).
If your app is installed to a system-level folder or you want a "completely silent" update then you'll have to use a Windows Service. See AutomaticUpdater tutorial for Windows Services and Console Apps or How to Silently update a Windows Service.
If you want a pre-written example Windows Service using the AutomaticUpdaterBackend then download the AutomaticUpdater source code. There's an example service inside the project.
Does this help?