@rsg You can treat them like they're all on the same zone for the sake of the calculation, and you can set the run time and get a decent number to put in for the area. The area value will lead to more accurate water usage estimates but doesn't impact your schedule.
What's more concerning is the impact on your shrubs and trees on being on the same zone and therefore schedule. If you work through the Water Use It Wisely site, you'll see that the watering needs of shrubs and trees can be quite different, but with your system you can't give each of them what they need. You have to pick one or both (trees and shrubs) to be optimized, and the other will suffer. You can try to find a middle ground, but at that point both will suffer to some degree. I'd suggest when you can afford the time to have someone install a separate valve with irrigation lines to your trees. I say that assuming that you have fewer trees so it will be less expensive than adding a shrub-only line.