From my experience, you cannot run multiple zones at the same time. I once had something similar going and the controller would get confused and then not water zones altogether.
Not sure I know why you need the zones to run at the same time, but you can have one program that runs all the zones, but each zone will run sequentially.
Say Program One runs at 3 am, but it runs Zone 1 for an hour, Zone 2 for 30 mins, and Zone 3 for 45 minutes.
Then set program one to run whatever days you want without worrying further about each zone.
So you only need to worry about the start time for the overall Program, and the length of time you want each program to run in there.