Yes, measure the effluent before it goes back into the tank. I put a small specimen cup on my fuge wall, drilled a hole halfway up the side of the cup. The line from my reactor drips into this cup and I have my controler probe in there, so it's reading the effluent ph and turning off and on the co2 accordingly. I've also put a timer on my co2 solonoid, so it stays off all night.
I use a ph monitor in the tank, so I can see both levels all the time.