You have to rig up an overflow system that brings water from the top tank to the bottom. Run the canister filter on the bottom tank, with the output going into the upper tank. Might take some experimenting to get it working right because the overflow must keep up with the output of the canister. If you intend to use a single chiller for both tanks, it must be connected to the canister's output. This basically turns your lower tank into a sump of sorts.
Long term, should the canister fail, your lower tank may overflow and flood the floor, so you have to factor in this when designing the overflow.
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