I have MCC and I don't do anything with population control. I don't mind what the game gives me. If I don't like a generated Sim I go to manage worlds and delete them. The game will generate a new Sim.
I have don't fill empty houses but that's game options. If not I changed it so no one moves into empty houses.
I let the NPC Sims progress on their own. I did notice that the same Sims marry each other and the offspring stays the same in every save. When I get a new pack and start a new save some partners do change otherwise they stay the same.
I only use MCC to make the days longer, no relationship decay and to keep marriages intact. Also, I adjusted motive decay to account for the longer day. I think I changed it to 50. I changed seasons to 14 days (or is that game options or the mod? I forget) and pregnancy lasts 7 days in my game.
I used the mod to turn off emotional death and I right click to give recipes to my Sim and do other stuff. I use the cheats on the Sim and mailbox by right clicking all the time. Usually for motive control before a party or something. Sometimes I use it to change a trait without going into cas and I sometimes use it to summon Sims. Everything else is left to whatever the mod calls default.
I don't do any flags or mess with skill rate, population etc.