i would not adjust root depth to adjust watering times.
if you search on this forum you will find exactly how it is used, but combined with soil type, percip rate of your heads it knows how much to water to saturate the root zone, which is all you are trying to do.
square footage is only used for estimating gallons used for the graph. do not consider this to be hyper accurate as some have.
when you define your heads, that is based on percip rate, which includes square footage and the count of heads as the percip rate is the rate at which water will fill a cubic square. the important part is to make sure your percip rate is correct, if it is not, iro proposes some pretty inaccurate watering suggestions. also, make sure your soil type is correct....that also has a big impact on run times.