The way you do it is by "surging" the water:
A surge (i.e. "pulsed" flow) is designed to simulate waves at the beach, so that the algae will get a dry-time (say, 15, 30 or 60 seconds, NOT minutes). Dry time helps kill the green and slime algae (which can't live out of the water), and helps promote the real red/brown turf algae, which spends half it's time out of the water anyways. The less hair and slime that collects on the real turf, the more the real turf can get light and flow and thus do its filtering. Dry time also helps remove the boundary layer of water on the algae, which otherwise tends to reduce the transfer of nutrients back and forth from the algae to the water. To further simulate the beach, a fan can be added that will help dry off the algae when the flow is off. The more air, the better. Note that for a fan to work, however, the water must be pulsed; continuous water flow will not let the air get to the algae. Also note that the fan will do a lot of cooling too. Note, however, that non-pulsed scrubbers that grow only green hair and slime still do a great job. They just grow a lot.
Original versions of scrubbers in the '70s, '80s and '90s used a tilting water dump-device (which was patented for many years) which filled up and dumped periodically. It worked but had many drawbacks, which fortunately are all solved by the current waterall design. The two current methods of pulsing the flow (i.e., surging) are by putting a timer on the pump (if you are using a pump), or by building a siphon surge device out of pvc, which works with or without a pump. The siphon surge method is not the easiest thing to build, so if you have a choice, try a timer on the pump first. Nevertheless, here is some info on siphons:
http://www.tiwalkme.org/BellAndSiphon.htm
Note that a pulsed flow is not required for a scrubber to work, and it's not even proven that it works better. However it does seem to be required to get real red/brown turf to grow, and it is this type of turf that pulls the most nutrients per unit size.