Not sure which instructions you're talking about exactly whether its getting the reactor tuned in or the settings on the controller. Once you get the reactors effluent coming out at roughly 6.5 when the solenoid is open and CO2 is being added then you will want to set your APEX similar to what the example I posted.
It requires a lot of testing for KH initially becuase the more your solenoid is open and dissolving your media the higher your KH will be.
So in essence you will be testing your KH and adjusting the 'on' time your solenoid is open.
I think initially (4 years ago) I used to run my settings around on when the PH hit 6.8 and off when it reach 6.65, but that depends on your corals needs. That link on page one gives some good information-this is from that link;
Open the needle valve on the side of the regulator to allow a bubbles to rise in the bubble counter. To start off, one bubble every three seconds is recommended.
Close the pinch valve on the effluent tubing so that the output is roughly 40-60ml per minute.
That should get you close to start off then its just a matter of testing, wiating 24 hours, adjusting, waiting 24hours, testing, adjusting, waiting 24 hours-it took me a week to get things dialed in perfect and that was 4 years ago
Look that link over, it will help a lot
THEN
Unrelated to the controller running the reactor you should look into testing your KH through the titration method using that second PH probe.
DIY Alkalinity test - Reef Central Online Community
Around post 15 I think its explained a little more clearly, you dont need to make your own acid. Basiclly take your 2nd PH probe that you will probably be using to just monitor the tanks PH, (thats what I use my 2nd one for) and place it in a container with 100ml of tank water, add the .1N sulfuric acid until the probe reads 4.20 as the PH, then multiply the number of mls it took to get to 4.2 by 2.8.
For me I use 3.2 mls of acid, multiplied by 2.8 gives me a KH reading of 8.96, its accurate beyond belief, no colors to mess with and the best thing, its CHEAP. I buy a gollon of acid for 50.00 and it is good for close to 1250 tests, ya 1250 tests for 50.00 with scientific accuracy.