Hey Johny,
I don't know if you're using a .NET app or not, but if so you can just use the AutomaticUpdater and your app will automatically start after a successful update.
Now, to answer your question. In wyBuild click "File -> Properties", and go to the wyUpdate tab:
[attachment=0]close-wyupdate-on-success.png[/attachment]
Click the "Close wyUpdate on successful update" check box. Now rebuild wyUpdate and include the latest client.wyc and wyUpdate.exe files with your app.