The substrate doesn't get stirred, I generally pour it into a bucket, add tap water conditioner, then use a maxijet 1200 to pump into the tank. I just ran some searches and some have recommended temporarily adding a UV filter, which I happen to have laying around. So I added an 18 watt UV to the water path of the eheim (tank-->eheim-->AM1000-->UV-->tank). I'll give an update tomorrow.
75 Gallon - 4x65w PC, HP CO2, Eheim 2217 feeding Aquamedic 1000 CO2 Reactor, Fluval 404, 18w UV filter (for emergencies), Peat Moss, Flourite, Eco-Complete and Onyx Substrate
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72 Gallon Bow Front Reef with 20 Gallon Sump, MH + PC Hood, Wet/Dry, Calcium Reactor, 11w UV filter (for emergencies)