99% of the box is submersed. The wave crest should reach just below the top of the box. As the pump turns on it pushes a lot of the water out of the box. When the pump shuts off, the box fills back up. It does this very quickly over and over w/ the frequency being controlled by the controller. The water being pushed out of the box and then let back in, constantly over and over produces this wave effect. This along with the length of the tank and how the water deflects off the opposite end of the tank will determine how big or small a wave you get.
Probably not the best explanation but the best I could do at this time of night.
Hope it helps.
Rob