I recommend an irrigation company to come in and audit your system
Generally for a homeowner it's best to keep your system simple
1 Program with only 1 start time
With that being said- Where i live a very general watering schedule is during the Months of May and June- an every 3-4 watering day interval and during the months of July and August - an every 2-3 day watering interval.
This of course depends on Hyrdozones and the Micro climates around your house ( Plant type, Soil type, Shade, sun)
It is generally better to water deeper, less often. The down fall to this is possibly run off from over watering . The idea is to split it up into a Cycle and Soak Method
For example- If a 4 zone system with 10 minutes of run time ran 3 times a week
I would split this up 2 or 3 times, instead of a full 10 mintues of run time- I would split it 3 times to a 3 ( or 4) minute run time over a 1 hour total run time
The down fall to this is if your zones are on a slope and don't have SAM heads installed this can cause extra run off.
An example programming if you want to get nice and detailed
Program A-
Zone 1 and 2 only
Run time 3-4 Mintues
Full Sun Zones and high priority front yard ( Because after all the whole point of a sprinkler system is to show off to your neighbors)
Start Time 1-6 AM
Start Time 2 -6:30 AM
Start Time 3- 7 AM
2 day water interval
Program B
Zones 3 and 4
Run time 4-5 min
3 day watering interval
Shade Zones and low priority zones
Start time 1 - 6AM
Start time 2 - 6:30 AM
Start time 3 - 7AM
Your controller SHOULD have stackable programming..
Programming can and should go even more in depth for properly watering