For your problem, CMARK, you can try changing the type of soil, or maybe the number of emitters for the problem zones. It’s trial & error, though. I don’t know the effects of the changes. One of my zones always waters in two segments with a short pause in between, presumably to allow the water to soak in… I’m not sure you can water once in the morning and again in the evening.
I have the same type of problem – I would like to trick the “smart” system to water more frequently. Here in Phoenix, we are having one week of 80 degree highs, and another week of 100 degree highs. The smart watering doesn’t water often enough during the hot weeks, in my opinion. There should be a way to trick the system to water more often.