In some environments an automated irrigation system can apply water faster than the ground can absorb it. This can happen frequently in areas with dense clay soils, soils that are hard-baked by the sun, and on land that is sloped. When water is applied too quickly, it doesn't soak into the ground, it runs off, in some cases straight down a storm drain.
To prevent runoff, water must be applied at the same rate that the ground can absorb it. So instead of having one cycle run for say 15 minutes, which might cause runoff, one could, for example, schedule three cycles of 5 minutes each, with an intervening delay of say 30 minutes. Water from the first cycle will moisten the ground and increase it's capacity absorb water. Water from the second and third cycles can then absorb into the ground instead of running off. Here's a good informative link:
http://www.snwa.com/html/land_irrig_cycle.html Be sure to watched the "cycle and soak" interactive on the linked page.
LawnCheck makes it easy to program in a "split-cycle." LawnCheck's "Multi-Cycle" feature lets you split a program into 2 or 3 cycles with an intervening delay with just one mouse click.