How long should I flood the tray? (flood duration)
Flood duration should never exceed thirty minutes total, from the start of the flood until the tray has drained back to the reservoir. Often times, the companies that manufacture ready made systems like hydrofarm, furnish those half hour increment "pull up" tripper type timers, simply because they're the cheapest item to furnish and not necessarily because they are the right thing for the best results with ebb & flow.
It is best to purchase an inexpensive digital timer to handle the floods, since they allow you to program better flood times. The optimum flood is just long enough to allow the flood to reach the correct flood depth, plus a few minutes to allow the nutrients to wash thru the planters, carrying away accumulated salts from the planters. Try to have the total time not exceed twenty minutes if possible, and never allow it to exceed thirty minutes total time.
With the megagarden for example: The system reaches desired flood depth in less than four minutes and drains away in about five minutes, so a ten minute flood allows pleanty of time and finishes the task in roughly fifteen minutes total.