Are you talking about using the AutomaticUpdater and you want to alter the beavior of the AutomaticUpdater restarting your app? Or are you talking about executing files as part of your update?
If you're talking about executing files as part of your update then just select the "Maximized" start style.
If you're talking about your app restarting as a result of the AutomaticUpdater, then you have to handle that in your code.