Hi Ariff,
Reboot system will actually reboot/restart the server. It is like stopping the server and restarting it. If there is a patch for the operating system for example that requires a reboot, then reboot system will be needed..
Restart amp will restart amp processes. It is like stopping an application and restarting it. The server will remain up only the application will restart. For example, if the webserver is not working properly, restart amp might solve it..