i generally make levels very improvisationally by kinda painting with tiles/objects in the level editor (usually game maker's room editor but i've made custom editors for some projects) then iterate on them by playing them repeatedly and changing stuff.
i rarely use a notebook for individual areas/screens but sometimes i'll use it to plan out the overall structure of a world. i have a notebook somewhere with the cat planet 2 world map in it for when i ever get back to that game