My set up is as follows.
Sanctuary: used as the primary base for my people. Have ok water and food, enough for the people. My defense says like 168 or so. I have a small 2 story house I build there, 1 prefab wood house, a basketball court, a communal "bath house", 2 communal bunkhouses, 1 area where I have a large generator and spaces for vendors once I unlock them plus some beds for them, 1 area for my Brahmin, a central choke point at the main bridge with 6 turrets and a search light, one the cement area next to the bridge I have a watchpost that will get artillery when I unlock those turrets, 2 guard towers watching the road from the bridge into the central commons area. My next project is a "bar" area.
Red Rocket: My personal mansion over looking sanctuary. Its 5 stories tall, and the only things I have there is Dogmeat and Codsworth or Preston depending on who I feel like taking with me. the 1st floor is a living room area with a power switch, terminal, some storage, magazine racks, and my collection of lunchboxes. The 2nd floor is a recreational area, with a bar and dining area, 3rd floor is my bathing area and food storage, 4th area is my bedroom with storage, tv, and a balcony area that goes around the red rocket, 5th floor is rooftop seating and watch tower.
I kind of feel like a rich overlord watching over my minions from a distance.
I do have a small house at the drive-in, outpost zimanju (spelling?), Abernathy farm, and tenpines bluff but for the most part I stripped those areas of resources and lugged it back to my main two areas.