During the setup period I would recommend to monitor the reactor, once you know the right effluent flow and CO2 bubble rate you can move it back to the main tank.
I do not remember which outlet is which but one comes out from the top of the reactor. That is the secondary one that you will set just to drip a little bit, say 4 or 5 drops per minute. It is just to prevent CO2 gas accumulation on top of the reactor so do not put it inside the water but above the surface so if gas CO2 comes out it disipates in the air rather than bubble in the water.
The other is the main output, that is the one of your main effluent. To measure it's PH, hang a cup on the inside side of the sump and let the effluent to drip into the cup, once the cup fills up it will overflow into the sump. Put the PH probe inside the cup and thats it. You will be measuring the effluent PH (Which is the one in the reactor.