When operating in the automatic mode, zone 1 will start at the time you has set as a starting time. It will operate for the length of time you has specified for it to run, then it will turn off and zone 2 will start and run for the length of time specified for it and so on. Usually in the manuel mode, zone 1 will come on when the start button is pushed and the system will continue through the cycles just like in the automatic mode. Perhaps your controller required you to manually advance the zones when in the manual mode. Try leaving the controller in the automatic mode, but manually starting the system.