Which tools do you use for organizing your thoughts?

Aspiring game developer here

Want to make my dream Metroidvania. However I've quickly realized using One Note ends up making things a bit cluttered and was wondering which apps/tools you us for piecing together your ideas?

Most ideally I'm looking for a very good map maker to give myself a concept for what the overall layout should be. Id also appreciate a convenient method of indicating which enemies/bosses and items go where.