Sometimes the administrator account that can install a service remotely might not be the user account you want to run your Jenkins agent (one reason you might want to do this is to run your builds/tests in more restricted account because you don't trust them. Another reason you might want to do this is to run agents in some domain user account.) This option lets you do this. If left unchecked, this Jenkins agent will run as the 'SYSTEM' user, who has full access to the local system.