Ok so what about this? Think about a wet dry and then could I just put a pump in the second section(after bio balls) and have it feed the algae scrubber? Or would it not be cleaning only dirty water so it would be ineffective? I could have the pump installed under the bio balls and feed the scrubber in the second compartment. Would that be better?
I wouldn't be concerned with 'clean' vs 'dirty' water in your system at any given point. To my understanding, the wet-dry should help with NH3/4 converting bacteria, but will leave plenty of NO3 in the water for algae to grow on your scrubber. Your algae grows via photosynthesis, which requires nitrogen (usually in form of NH3 or NO3), phosphorus (usually in form of PO4), light, and a few other elements, such as iron, potassium, and some other smaller trace elements that are not as likely to be limiting factors.
Point being - your system will most likely have plenty of nutrients for your scrubber to consume.
Ultimately - as far as design goes, get on the ATS basic thread and figure out flow rate, size, lighting requirements, etc, and then figure out where that will fit into your sump. They are typically easy to DIY, but sometimes challenging to fit into existing systems. Many times the most challenging part is to fit lighting in, so knowing the type and size of your lighting is important in this process. Also mentioned is the upflow scrubber which is a good idea for those who cannot fit the waterfall scrubber in place.
If there is no room in the sump, and you definitely want to do the waterfall style scrubber, your previous mentioned idea of pumping water up into a separate container will work, you will just want to gravity feed from the above tank back into your sump vs trying to use two pumps. You asked for a diagram in your PM. I was trying to explain something like this:
