I recently also tried to time the arrivals with the departures on my hub in Wuhan (WUH). For the short-haul flights though I just add them back to back as CBE described. If you have enough frequency, then you don't need to have specific waves for shorter flights where you have already direct demand.
For destinations though where direct demand is limited, you definitely need the connecting pax. On my long-haul flights I have basically 100% connecting passengers, as the direct demand for passengers to fly to Wuhan is very very limited.
As I operate with two different long-haul types (787-9 and 747-8I) I had to create a connecting window of around 3 hours. That means, I try to have my long-haul fleet arrive starting from 20:00 (up to around 22:00), while my earliest long-haul departure is 21:50 up to 00:00. My min. transfer time is 1:00 only. Using this 4 hour window also avoids having any issues with the slots. You can easily time the short-haul flights to arrive somewhere in between. I also tried to time my maintenance windows (at least some of it) during that long-haul wave window, allowing for arrivals before and departures after the wave. This way, I can feed passengers from smaller airports to my hub, allowing them to fly out to the world, and late night I fly back to the smaller airports taking the arriving passenger from the long-haul flights out to my network.
Pax will happily transfer if the transfer time is less than 3:00h, if it's above that, you will loose them. Though I believe some even take longer connections, but not sure about this. Also keep in mind, that Pax will fly a detour of up to 2x the original, direct distance, using a connection. So for example you won't get connecting passengers MUC-FRA if your hub is in CDG, but you can bring all German Pax to Spain for example. Keep that in mind, if you have to schedule some flights and give up some connections. I for example made sure, that European flights can connect to my flights to Australia/New Zealand, while I didn't care for connections from Europe to North America. For this it makes sense to have the Hub ideally being somewhat in the center of your network, so you can get most out of the connections. If you have a hub in New York for example, it's much harder to get connecting passengers as they will fly a much longer route in most of the cases, if it doesn't even make it impossible. So Denver, Atlanta or Dallas would be a much better joice.
Constraints like already full airports, night-time restrictions, etc. will keep the whole excersise challenging. Using the new connecting pages already available on Quimby will really help to fine-tune your hub, as you can clearly see where you loose important connections and can possibly re-schedule a flight by half an hour to allow a connection for 10 more flights.
I normally also try to have fligths in the morning and evening to allow for business passengers travel to a destination the same day, though I believe in AS this has no effect. The Pax simply use any flight throughout the day and don’t care at what time it is, yet for me it satisfies my pride…