i am pretty sure that the pH controller is for your calcium reactor and not reading tank pH (which you would use just a pH monitor).
thus, you want to measure your calcium reactor effluent pH.
how i made mine was to use a short 1" section of pvc. glue an 1" endcap on there. the length of pvc should be at least half as long as the pH probe because you dont want the probe falling out of the pvc.
i then super glued the effluent drip line to the inside of the pvc pipe. i then find a place where i can hang it and see the eventual effluent drip rate. thus, the effluent pH can easily be monitored.
set up your calcium reactor as per directions. effluent control is very important (as is co2 bubble rate) and the cheapest and pretty darn good effluent valves are the irrigation valves you can find at home depot (i just found them).
http://www.homedepot.com/webapp/wcs...catalogId=10053&N=5yc1vZ1xhcZapw5&R=100139352
i would get your ca reactor set up and running WITHOUT running co2 yet. play with the effluent drip rate, get familiar with everything for a day or two. the world will not end in those two days.
measure your alk of your tank at several intervals of the day...just before the lights come on, when the lights come on, the lights halfway through its cycle and at the end of your light cycle. this will give you an idea on what your tanks alk consumption is.
now for co2...
adjust your effluent to about 1 drop per second. your pH controller should be set to turn on when the pH reaches 6.6 to about 6.7. starting bubble rate at 1 bubble per 10 second. this is the hardest thing to set up for a ca reactor. getting the bubble rate and effluent rate where you want it.
now, watch your pH controller. the pH of the effluent should be very very slowly decreasing for tank pH to a reading that is inside the reactor.
'once' the reactor reaches its target pH (for dissolving media), measure the effluent alk. it should be about 40'ish. too high and your bubble rate is too high. too low and your effluent rate is too fast.
now you know why you should practice for a couple of days with the knobs and such. this will give you an easier understanding on how to play with them.
now...
once you get your alk effluent consistently in the 40's...
remember all those alk measurements you did before the intro of co2? well, now you can slowly increase the effluent/co2 rate SLOWLY to watch your tank alk rise SLOWLY. this is why the before and durings and afters are so important.
measure your tank alk several times a day over a period of two weeks to fine tune your ca reactor. after this, it is pretty much leave alone with testing alk once or twice a week.
notice i didnt mention testing calcium once? you could. i do about once or twice a month. BUT a ca reactor is actually erroneously named. it really should be called an alk generator. when you generate the alk, a calcium molecule follows. alk is much more important in tank stability than calcium.
how did i learn all this? the hard way. it wasnt until an experienced reefer friend showed me the proper way.
good luck.