I would create a service and if updates can run the application file together with a command or when updates to be downloaded to run a file under one command.
See: Executing files in your update
I would like to create a service wyUpdate low vb net. I wonder if there is any open source on this already. I'm reviewing the tutorials and I am not very clear how to develop it.
Best advice: don't do it. Just use wyUpdate as a standalone updater. Hiding wyUpdate in a service doesn't make things easier -- it makes things harder. And it gives less transparency to the customer.
But if you're determined, here's the place to start: http://wyday.com/wybuild/help/faq.php#silent