You always want water flowing through the reactor... what you turn on and off is the CO2 being added to the reactor via the solenoid.
You use the AQ jr to monitor your tank's pH, and set it to shut off the solenoid for adding CO2 if your pH drops too low. So basically, CO2 is ON unless the pH drops too low.
You want something like this, in this order:
IF time > 00:00 then CO2 ON (so CO2 is always on first)
If pH < 08.00 then CO2 OFF (if pH is too low, turn off the CO2)
MAX change 010M then CO2 OFF (when CO2 turns off, keep it turned off for 10 minutes. This prevents the solenoid from turning on and off really fast if the pH is hovering around 8.00)