My system is on a pressure regulator, and I see very little variation in flow rate run to run, since my trip point is set to the default and it has never alarmed yet.
Therefore, I used the calibration gpm, square footage and an excel spreadsheet to calculate the nozzles inches per hour. As everyone noted this is not rocket science, and excel did the job just fine. I then entered the resulting data into the advanced data for each zone. The calculated nozzle inches/hour were in some cases quite different to the original guesses based on nozzle type, and so now I feel I have improved the accuracy versus just guessing.
Of course this calculation does not take into account all the on the ground variables like nozzle overlap, pattern variation and so on, but only rearranging the nozzles will fix those types of errors, and it will never be perfectly uniform no matter what you do. I am just trying to get close.