At the risk of confusing you more...
The CO2 line should go...into the bottom of the bubble counter, then out of the top of the bubble counter and into the highest fitting that is near the pump.
The input water line goes into the other fitting that is right near the pump.
The output water line connects to the top 1/4" JG fitting. I notice that the valve is sitting on the table beside the reactor. That valve is usually installed right into the top of the reactor. If the valve were installed, the output water line would be connected to that valve.
If you don't have a pH probe, you'll need to close that other, larger hole at the top of the reactor.
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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