It is best to have each pump on its own channel. There are 4 basic modes, Pulse- all pumps on and pulsing between two speeds you set 30-100% at a pulse interval from 1-7 seconds that you set. Interval 1, one channel on, one off, channel that is on pulses. Interval is from 1sec-12hrs between channels. Interval 2, like interval one but rather than turn off the other channel idles at 30% power. Sequence, really only useful with 4+ pumps, pumps turn on in sequence.