Generally it's better to just "Rest" during the night period, especially in Dark Forrest.
And when you sneak and aren't seen then they will just walk like you weren't there unless you make noise.

Enemies also shouldn't be spawning near player buildings/structures, so placing crafting tables on the piece of land you secured will make them unable to spawn in your vicinity.
I usually also dig around my base to make a trench so they won't just run in and destroy the crafting tables where I plant trees and stuff.