Blue,
Here is an example on how to set up the timer. Program A will start at 5:00 am and run zones 1, 2, and 3. Each zone will run for 10 minutes, which is 30 minutes of total run time. Program B should be set to start at 5:45 am and run zones 4, 5, and 6. Each of those zones runs for 20 minutes each, which is another hour of run time. Program C will start at 7:00 am and run zone 7, 8, and 9. Those zones will run for 5 minutes each. Leaving a 15 minute gap between the end of one program and the start of the second allows the system shut off and then restart with the proper program running. When manually running the zones, you need to make sure you are switching between program A, B, and C depending on which zones you want to run. If you leave it in A, it will always manually start the A program.
The other option is to start with just program A and set the run time for all of the zones. This will start with zone 1 at the designated start time, run it for the desired time and then switch to zone 2. This will continue through the duration of the programmed zones. When the program is completed, it will shut off and start on the next scheduled start time.