Flood and Drain systems also known as Ebb and flow systems supply water and nutrients to the plants by periodically flooding the bed / grow tray. The water / nutrient solution is stored in a reservoir and the water is continuously drained back back and forth from reservoir and the root zone / grow tray at predetermined intervals.
The grow bed should be level and uniform for the even distribution of the nutrient solution. Lopsided uneven beds / tray create multiple problems. Some roots can become too saturated and not drain adequately, leading to rot and poor oxygenation. Other roots will not receive adequate moisture and solution which leads to nutrient deficiencies.
Adequate levels of oxygen are essential not only to plant vigor, but their very survival. With ebb and flow hydroponics system it's imperative that the roots not be in the solution for any more than 20 minutes to 1/2 hour at most. Leaving the roots soaking too long creates an 'anaerobic ' environment, basically the plants drown.
Some people will fill the entire grow tray with grow media, this is not really necessary, is a waste of resources and creates unnecessary labor in cleaning excessive media. Net pots themselves can be filled with media which works just fine. Another method sometimes used is rock wool slabs in conjunction with clay pebbles or similar media, the rockwool is set atop the pebbles. Avoid ultra light media that will float as it can easily foul things up in a flood drain / ebb flow system.