I do recall the 2nd chamber is for scavanging excess CO2, so that you can run the first chamber pH really low to melt more dead coral without dropping the tank pH which would inhibit living coral from using that good stuff. Some guys used coarse medium in the 1st chamber so it didnt melt so fast, fine in the second so it got the rest of the CO2 so they would decrease the same amount and they can be changed put at the same time.
What kind of regulator are you using? Without a good regulator it will difficult to keep your your ph in the reactor steady