The reactor input is facing towards the drainage from tank to sump, the output is either directly plumbed into the skimmer pump or extremely close to it. That way all the water exiting the reactor will be skimmed right away for all the excess bacteria produced by the pellets. over time, slowly(once every couple of months) inch the reactor output away from the skimmer till you have about 2 inches of play....that way your tank can slowly adapt to the extra bacteria thus reducing the chance of a crash happening again!
Non the less, I really hope everything pulls through for you!
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