I can't say I know the best way, but I have two on either side of my 150 and I run them in the purple mode (Tidal Swell), one pump set to the opposite of the other.
Basically one pump ramps slowly up to full, then back down while the other ramps up, then both ramp up to full, then both run slow for a for minutes of calm before it starts all over again. I used to run in reef crest but it always seemed like the pumps were idling.