I am thinking???

Depends. You could keep the canister flowing for additional water movement and the ability to add a different variety of media if needed down the line. Which would be a bigger pain--taking it out, or leaving it in?
 
People put macroalgae in a part of their sump called a "refugium".

Macroalgae absorbs phosphates and nitrates (bad stuff). The refugium also can grow various types of "pods" - little bug-like creatures that fish like to eat and also help process detritus.

A refugium is a "refuge" for both the pods and macroalgae from the main tank as they would probably get eaten too quickly by the fish to do much good.
 
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