You want the air to run constantly (unless you want to turn it off during a tank change but I leave mine on). As for the water, once you get the plants going, I say keep the water fed constantly as well. Prior to that, however, I would suggest a timer. For my grow, I was originally running my water pump constantly at first (from the moment the seed was dropped in the RapidRooter). Once the sprout came up, I put my pump on a timer. I set it to come on for 15 minutes ever 6 hours while the plants were young sprouts. As they got bigger, I swapped the schedule to 30 minutes every 3 hours. Once the tap root was in the main reservoir and there were roots out in the clay pebbles, I swapped over to 24/7 operation.