You bring the DKH of the reactor down by increasing the CO2 bubble rate. In short, the more CO2 you add to the reactor, the more acidic the water is inside the reactor and the media starts to dissolve more. The 6.3-6.5 range is a ball park range...you can go higher than that depending on your tank demand..but not lower because the media will turn to mush. In my opinion, you can ditch the controller portion of your controller and use it as a reactor monitor for now.
Once you get the reactor pH to whatever you desire, take Ca and dKH readings of your tank. Do this daily. If you notice that the dKH of the tank is going up then you will need to lower the CO2 bubble rate..if the dKH of the tank is going down, then you will need to increase the CO2 bubble rate. Keep tweaking the bubble rate until your tank dKH no longer flucuates...it should remain constant..thats the goal. After its constant then use additives to raise the tank dKH or Ca if needed to the levels desired. The reactor should keep the values constant thereafter until you add corals or they grow up big enough to need more Alk and Ca.
If you want to use the controller, you should put a probe in the tank and tell the controller to shut off the CO2 when the tank pH gets down to 7.9 or something close to that. Hopefully that helps.