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I've got an Eheim Pro II 2026 hooked up to an 80g tank in much the way you describe except without the overflow. I wouldn't worry about any agitation with the overflow since the Eheim is basically a closed loop. There won't be any uncontrolled/open system cascading down the overflow since it has nowhere to go if the pump's not running.

Anyway, a word of caution about current. You're better off splitting the intake into both holes and using the spraybar that comes with the filter as an output. The pump on the Eheim isn't sufficiently powerful enough to make a current in a 90g tank unless it's choked back a lot. I have to have use powerheads in the tank currently in order to get enough water movement. Rather than use the spraybar another option is to just have the U tube in the tank and direct the flow from that horizonally with the attachments provided.

Even with that your best option is to get two filters and have one hooked up to each hole.

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