After guests exit a skyliner car, instead of new guests entering, a CM sprays the car. The car is empty until it reaches the next station. That few minutes should be enough time for the disenfectant to do it's thing.
It's self explanatory and also lewisc's explanation.
Gottcha, only loading the skyliner with half of the people capacity. I thought they were saying only run it one way or only open half the lines or with half the cabins and I couldn't figure out how that would help at all. But loading every other cabin and disinfecting alternating ones could work as long as the disinfectant could be applied in the ~30 seconds the cabin is in the station with its doors open after people exit