I'd probably group by like zones, especially for cycle/soak. If using cycle/soak best to have zones with similar watering durations. If you have wild variations in watering time (i.e. tree 3 hours, grass 30 minutes) there will just be too many cycles.
I'd also start with maybe a zone or two just to see how they system behaves and that could help dial-in other zones.
This FAQ might be able to answer some high level questions.
Hope this helps.