RGibson,
You cannot control the "speed" of the box, if you are talking about a Stream where you can adjust from 30% to 100% power. The wavebox can only be adjusted for the duration of time of the pulsing on and off. When it is on, it runs at 100%.
You need to play with the timing to find the right pulse timing for your tank, otherwise you wont have a wave like effect, it will just be random bouncing water.