Ok, I have started trying to plan out my plumbing, and have a fairly basic initial diagram. Granted at this stage it doesn't show any check valves, unions, or most other valves that would be in the system. I think of it as more of a high level diagram to get the basic flow and denote the location of various pieces of equipment.
So, waste water starts from the 180, goes through the red lines to the primary sump. Then a pump (purple-ish box) takes water via the orange line before the skimmer in section S2 to the refugium, where hopefully the macro algae and rock further cleans the water returning it to the secondary sump via the yellow line. The Green lines then take the water from the sumps back up to the main tank (or transfer between the two sumps if there is a flow imbalance). The water from the second sump is also passed through a UV-Sterilizer that is in parallel with a gate valve. I figure at normal operation the gate will be closed passing all the water through the UV and killing stray alga and perhaps some bacteria, but when needed, I can open the gate to reduce the flow rate through the UV to kill protozoans. Since the filtration of the main tank should turn water over close to 5 times an hour, even with the gate open, the UV should see around 200->250 gallons per hour.
I am planning on two ~500 gallons/hour pumps to return water to the main tank. That way I have some redundancy so I can take one offline while performing maintenance, or if a pump fails, I should still have close to 2x/hour filtration.
I figure I should be able to place heaters in sections S4 and S5. Currently I am not sure what to do with section S3, or where the output from dosing pumps should go. I would appreciate suggestions regarding those items. Also, does anyone see some issue with this flow plan?