Available Flow
In any case, you need to measure the flow rate. Do this step. It is critical. Do not, I repeat, do not calculate the flow rate based on pump curves and head-feet of pressure. This may sound like a total pain in the behind, but just trust me on this one. Would you rather go through all the effort of building a scrubber, only to have problems and find out that you didn't have as much flow as you thought you did? Believe me, I've been there.
If you've been reading this thread, you will see that at some point I started making a big deal about this. The reason is that it is a big deal and I think many people don't realize that their pump does not pump at the rated flow, and in the majority of cases, it doesn't come close to the flow calculated by using a standard head-foot calculator program or table. So I have chosen to make it the #1 priority for scrubber design, hands down. You have to know your actual flow.
For a drain fed scrubber, fill a pitcher with the water entering the sump. You will probably need to rig up a temporary pipe or routing configuration so that you can fill the container. For a pump-fed scrubber, set up the pump in a sink filled with water to the same level as your pump will be submerged, and connect the tubing required to reach the height of the connection to the horizontal slot tube, so that you mimic as best as possible the actual conditions. Backpressure created by the slot/screen is negligible unless your flow rate significantly exceeds 35 GPH per inch of slot length.
Now that you've done all this, fill the container and record the time it takes to fill it. Do this at least a dozen times. The way I do this is by using a recording device, like a digital voice recorder, and just calling out "Go" and "Stop", then afterward, playing it back and using a stopwatch to get the time intervals. You could also have someone else run the stopwatch and write down the times. Average out the times and then figure out how many gallons per hour of flow you are actually getting. If you have multiple drains, measure and extrapolate GPH for each individually, and then add together.
For instance, if you are using a 1/2 gallon pitcher, and it takes 4.5 seconds to fill it, then you would have (0.5 gallons / 4.5 seconds) x (3600 seconds / 1 hour) which would be 400 GPH.
Don't be surprised if you have a lot less flow from your pump than you thought you had. I had less than 1/2 of what I thought it was. Head-feet calculations are usually way off, because most people don't use big enough return hose or have other restrictions in the plumbing. Some of it is inherent to reef-ready aquarium design (1" drain, 3/4" return, Danner Mag-Drive 9.5 and larger pumps need 1.5" return, see a problem?). So don't feel bad. A lot of people are in your situation, but they just don't know it.
Start with a clean pump. If your pump is not clean, soak it in vinegar for 15 minutes and scrub it good. After running a scrubber for about 4-5 months, your pump flow will drop about 15%, and by 6 months, it will have dropped by 25%, so you want to know your best-case flow and build around that. It's a lot easier to start with a throttled-back clean pump and open it a little when the flow rate decreases. Figure out your system flow rate, multiply by 80%, and that will be a good starting point. But, it's not going to kill you to start at full flow, and end up with a little less over time. You might just want to clean your pump a little more often, say every 3 months. So it's up to you. Just being aware of your system conditions puts you miles ahead.