40g breeder sump setup

I could put the intake, skimmer and reefmat in the same section and just have a huge refugium section with a egg crate bubble/chaeto trap baffle right before the returns.

I'm running 2 sicce 3.5 btw
 
You will probably have algae growing on your ReefMat causing you to burn through more mat.
 
You will probably have algae growing on your ReefMat causing you to burn through more mat.
So separate the reefmat.

How about reefmat and skimmer in one section on their own, then the refugium, and then the return section?
 

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