Area: This has no impact on your watering and is used only by Rachio to give you an estimated amount of water used. To be honest, I wouldn't even mess with this out of the box. Once you feel comfortable that your Rachio is watering your yard correctly, then you can play around with this setting.
Root Depth: This will default to the type of plant you have set for the zone. So if it's a tree only zone, it'll be one lenth, if it's a shrub zone, it'll be 15" i think. I would leave it for now on the default for whatever plant type you set.... example: your shrub zone will default to 15", and Rachio will water to a depth of 15" every time.
Allowed Depletion: default is 50.... basically it says that your Rachio will water when it thinks your soil is about 50% depleted of moisture...I believe Rachio uses this number because it's been shown to have the best effect for plants... i keep mine at 50.
Effeciency: how effecient is your zone at putting the amount of water out that it says it is... not as big of a deal with drips (used more for sprinklers), I'd just keep it at 100 since your drops are appropriately placed at the plant.
Coeffeicient: How fast does your plant use up water resources, it'll deafult based off the plant setting.. again, i'd leave it alone assuming you have the correct plant setting, you can tweak it once you get a feel for the system. You'll noticed shrubs have 0.5 vs treets of 0.75.
Some people say put a 1 for each emitter.