Be sure to take a look at the Web Soil Survey website, and find your soil type and the associated 'Available Water (AW) value'. This is very important for your scheduling. Set your Area of Interest (AOI) from the map, then use this post to find your soil type and associated AW number. Once you have the soil type and AW number, set both of them correctly in the zone setup.
I would think that you'd be better off with fixed flow emitters, but @Linn could probably guide you better. I don't have those plants and am not sure of their requirements. If you have some that are quite a bit more mature than others, it's better for the plant to have multiple emitters spread around the circumference of the root ball.
If you're using the existing 'emitter' nozzle you are likely under-watering right now due to the precipitation rate (PR) default setting for the emitter nozzle, which assumes that you have emitters spaced out evenly and continuously. Take a look at this post to dial in your emitter based zones.
Again, @Linn may be a better guide as to how many gallons to deliver. The 'Water Use It Wisely' site is for Phoenix, so your mileage may vary. Before going through the PR calculation process above, you'll want a reasonable estimate of your root depth and soil settings first ! Rachio will make a schedule with an 'inches of water' number, and you'll use that number to calculate the PR.
Once you have a custom nozzle with the PR that you calculate from that description plug it into your zone. You should then see your duration match your target watering time.