I try to keep true to the spirit of the settlement, if it has one. If there are existing features like farming areas I try to reuse them for agricultural plots, or if there are existing buildings I try to reuse them if possible. If there are already people living there I tend to leave their stuff alone, and just clean up the trash and debris and build around them.
For example, in Sanctuary I left the Sole Survivor's house and the workshop house alone. I scrapped everything else, and placed residential plots on the existing home foundations around the cul-de-sac, commercial plots on the foundations nearest the bridge, and replaced the streetlights. At The Castle I fixed the walls with a mod, put a row of residential plots along each of the outer walls, and ran a boardwalk in front of each row. There's some commercial outside the main entrance (focusing on food, medical, clothing), and the agricultural plots are inside the walls. It's also heavily fortified with a perimeter wall and martial plots.
I use a lot of temporary pieces when building, mostly wooden floor pieces for spacing and lining things up. Place Everywhere is absolutely essential for getting things where I want them, particularly for moving objects up and down to match the terrain.