The pH probe can go directly into the reacor chamber on some units if they were designed to do so or like I do which is drip the effluent into a Lee's large specimen container hanging on a sump baffle and sticking the probe into it. the container is like the one they use to catch and bag fish in at the LFS that hangs on the side of the tank. I cut a narrow strip of clear acrylic that reaches across my sump front to back and drilled a 5/8" hole in it to suspend the probe over the container.
I would not feed my reactor from the drain or overflow since it contains food and wastes and will soon foul the calcium media. You want a clean water supply like the return or a seperate small pump, I use a MJ400 powerhead with the sponge on it to keep it clean. You will also have a recirculation pump which moves water around inside the chamber so the low pH water comes into contact with the calcium media.
My reactor starts and stops automatically based on the pH in the Lee's effluent container, when the pH reaches a setpoint like 6.7 or whatever you choose the CO2 regulator solenoid shuts off but the water keeps recirculating until the pH rises to 6.9 or whatever where you feed CO2 again to lower the pH. 24/7/365 once you get the CO2 bubble count and effluent drip rate set properly.
I never shut off anything associated with water or pumping in my systems since still saltwater can go septic very quickly and cause problems. Maybe for a few minutes while feeding or doing maintenance but not overnight if it holds water like a reactor, filter, refugium or sump. The reactor is not meant to control tank pH but to add needed calcium and alkalinity.