Putting a PCB module on a PCB is not unusual these days as module manufacturers can make them much cheaper that you can buy the parts for, and it’s tested too.
You just need to make a symbol that’s a rectangle with its pins. A giant part if you like. The footprint is just the rectangle for the module and the connector pins in the right places. Chances are somebody has done them for such a common module and you need to search the Internet for projects using it.
You will not be able to simulate in Spice a complex module such as a microcontroller. Generally you just use firmware to tailor its behaviour.