Well, the first step is to read the step-by-step walkthrough article. Then, you can integrate the updating into your service a couple of ways. The best way for you (since you're using a .NET app) is to use the AutomaticUpdaterBackend (see: AutomaticUpdater tutorial for Windows Services and Console Apps).
Just for reference, if you were making a non-.NET service you could use wyUpdate in standalone mode (see: How to Silently update a Windows Service).
After integrating the AutomaticUpdaterBackend within your service everything should be automated. You're completely in control of when it checks for updates and how often the updates take place. Also, it will all work without user intervention.
Tell me if this helps.