That is the setup I use. Two timers one for the pool pump and one for the booster. On the timer that handles the booster add an extra off tripper on the dial for a half hour before the main pump shuts off. That way if you are running the booster after its normal run time at least the booster will shut off before the main pump shuts off. I believe you will damage the booster if the booster is run without the main pump.