Hi Scott,
To my knowledge there isn't a way to run a cycle on every 3rd day. The reason we didn't implement every N day on LawnCheck because most people want to know which days of the week their sprinklers will run - especially in mowing season.
You can more closely estimate an every-third-day schedule using two programs: set one program to run on a 3/4 schedule, for example Monday and Thursday, and then create another program to run once a week, for example on Saturday. You can scale back the irrigation times on the Saturday programs as needed. This will give you a 3/2/2 schedule
Hope this helps.
Jim