First of all you shouldn't empty the tank because you are basically killing all of the benificial bacteria that lives on your rock and bio filter, and it is not like your running another system because most of time there are no fish to create waste. I have a 14 gallon bio cube as a quarintine tank, and I have bearly touched it and never had a fish die in it.
BUT, you could use Aqueon Aquarium Water Changer wich is a hose from your aquarium to the faucet where the water can exit from the Drain
Hope this helps!
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