The general idea is that when the lights in the main tank are on, there is photosynthesis among the inhabitants in the tank. This breathing helps to keep the pH a little higher but it drops at night when the lights go off. If you bring a scrubber on line during the off hours then the peak breathing in the scrubber will compensate for the drop off in the main tank.
This should smooth out or dampen the pH swings that occur during the day and night. Sometimes you need to have the two over lap or conversely, you might have to have a lag between the times that you turn on the lights in the two systems.
It may only be because people don't fine tune but many people do over lap, having the scrubber on about 14 to 18 hours a day with the middle of the light period of the scrubber being in the middle of the dark period in the main tank. ....but there are no hard and fast rules.
Sometimes, the pH regulation takes a back seat to nitrate control so that, users often increase or decrease the length of the light period according to the nutrient level that they want. The current fad outside of the scrubber world is that CO2 is a major player in pH control. If the lighting in the two systems over lap, the CO2 stays relatively depressed so the effectiveness of the counter lighting still works well.