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I use a canister to run phosphate media in (I had it laying around). Take all the media out of them. I think you should only use carbon and phosphate removal in them, and change those frequently. The sponges in canisters are nitrate factories, take those out or clean them very well every few days. If you've got ammonia, then it definitely sounds like a cycle, wait it out, the above suggestions re: the canisters will avoid any future nitrate problems. A skimmer is always a good idea, and you can definitely use the canisters just for flow, just make sure the floss/sponge whatever is gone, along with everything else.
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