First, don't worry about pH harming the fish. The pH changes that occur from CO2 dissolving in the water have not been found to harm fish at all. Also, you can't determine how much CO2 is in a typical aquarium by measuring pH and KH. To use the controller you should determine that you have the right amount of CO2 by another method, such as by noting that you get some pearling within a couple of hours after the lights come on, and not so much CO2 that the fish start clustering at the water surface like they are gasping for air. Then set the controller to control to that pH, whatever it is. You can still experience a change in KH, such as by dissolving carbonate rocks in the aquarium or by having Vals or other carbonate eating plants in the tank. That will make your CO2 level change when the controller holds the pH constant. So, you need to observe the tank carefully every few days to make sure you still are controlling to a good level of CO2.
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