When you use multi-cycle you'll see the word "Auto" as an option for inter-cycle delay. It's in the same drop-down selection box as "30" and "45."
Auto simply provides a 15 minute intercycle delay if you choose to split your program into 2 or 3 cycles. This inter-cycle delay provides enough time for water to soak into most soil types.
If you have sun baked clay soil, you might need a longer delay. If you are watering trees the cycle time is usually longer so you may want to split that cycle up and use a longer intercycle delay, like 30 minutes, or 45 minutes.
The "Auto" setting works well in most applications.