Wave system works more or less like this (the planning part; how to make PAX transfer is another story):
Departure from your hub at f.e. 8 am - all planes are leaving at 8 am (to North and East let's say).
That means that all your incoming flights must arrive until 6:59 am (if your hub has a minimum transfer time of 1 hour).
Next wave would be f.e. 4 pm - all planes are leaving at 4 pm (this time routes to the South and the West of your territory).
That also means that all your incoming flights must arrive until 3:59 am (if your hub has a minimum transfer time of 1 hour).
If a third wave is possible, depends on the route length you are flying. In the beginning you will perhaps even fly 4 waves (with very short to short routes).
Hope this helps.
Lets say the first departures of the day is at 0300 , and minimum transfer time is 1 h15 .
should those flights be back at 0645 , for the 0800 departures ?