Pretty much as you described. I got an empty sized case and seated a spent primer so water wouldn't leak out of the primer pocket. Weighed the case empty, zero'd the scale, then added water until full.
Add in your various other particulars (case length, seating depth, bullet of choice, barrel length, etc.) and then let 'er rip.
Keep in mind the program is just approximating pressures and some powders are better calibrated than others, but it will get you ballpark. It has been pretty accurate so far for my uses.