It's an
ebb and flow. Let the water rise about half way up the bottles, making sure the roots get a good watering, but don't let the water go higher than the top of the medium. The over flow pipe keeps that from happening if it is set at the correct height.
Once the roots are watered, about every 20 or 30 minutes with
grow rocks, the water should be drained right away. The overflow pipe allows you to water longer because most timers only have a 15 or 30 minute on time. But by know means do you have to water longer than it takes to wet the roots. A good cycle timer is a must for ebb flow gardening.