If you are talking about a RKE or RKL and I remember correctly it might only work with the APC module. That module works with specific pumps. I had MP10's and I do not use any of the wavemaker functions on the DA controllers.
I went on my RKE head unit and found I could use the pump function and set a output as WM A through WM C. A and B cycle back and forth and C and D cycle back and forth. In menu under general there is Wave Maker A/B and Wave Maker C/D. Selecting one of them will let you set the amout of on timer for each. It also has a random setting. If I remember correctly that will randomize the amount of time each is on with the max at the setting but I am not sure on that. I think the RKL has only A/B set.
I tried it before I posted. Which head unit do you have? On the RKE you press the menu button and it comes up in the general menu. The first chioce is Wave Maker A/B. See photo below.
Select that like in the photo below.
Press the enter button and you get the screen below with time settings. I set them at 30 seconds each just to test it.
I don't have a RKL so I cannot give you the keystrokes to get into the wave maker time setup.
There sould be a way to set the times for A and B it should be in the menus with night mode times in myReef if that helps. I don't have access to myReef at this time. I have an Archon and it does not use myReef. I will check my old notes and see if I find something.