Keep in mind I have had this reactor for a long time and the details of its operation are a little foggy.
CO2 does accumulate in the first chamber. If I recall correctly, this is to lower the PH and break down the aragonite (effluent) which is then pumped into the second chamber. The second chambers purpose is to help raise the PH back up before entering the aquarium. I have always been told dual chambers make a better reactor.