The first thing to do is to set all of your zones as accurately as you can. Schedules simply take information on each zone, calculates how long and when to water, and does that. But zone information is most important.
Be sure you specify the right soil. If not, too much or too little water will be applied at one time. I personally only use Flex Daily, as it takes into account actual weather conditions and rainfall in your area.
IMHO, the problem with most irrigation system recommendations as to how much water is required is that no one knows your actual situation. Maybe not even you. When choosing the type of sprinkler head for a given zone, I’ve found there is far more variation in the installation of the systems (how many heads, spacing, etc.) than the recommendations can account for. Using Catch Cups (I’m sure there’s a method here somewhere) is quite accurate, but there can be a lot of variation (and work) in doing that. I’m lazy, and I’m an engineer, so I prefer the method of measuring the square feet of each zone, and then measure the water applied to each zone for a given time, and using that calculate the ACTUAL sprinkler inches per hour. By using that value in the Advanced settings for a zone, I feel you can get much closer to the actual times required.
Anyhow, after setting all your zones, simply make a new Schedule by selecting the type (Flex Daily, for me), zones you want included, any restrictions, etc. and the schedule will be created for you. No, you will not normally have a separate schedule for a zone; a schedule can usually handle all your zones.
A Hint: If you disagree with the times the schedule comes up with (most will at one time or another), do NOT change the times manually, as the program will then quite calculating times when factors change. You’ll usually find times calculated are good, or at least close. If the time varies too much from what you have been successfully using, ask here about what to do, don’t just go changing it.
Hope this helps.
Oh, to calculate zone sprinkler head flow:
Inches per hour = (GPM / Area in sq ft) * 96.25
So, 12 GPM on a 1000 square foot area gives 12/1000*96.25 = 1.16"/hr