If you are using Sphinx for documentation thinking about the directory structure is important because changing it later gets painful. The builders replicate the directory structure in the source directory in the build directory so if you want to change it you will have to make redirects for the HTML documentation.
In my experience the following structure is rather flexible:
Documentation directed at users such as tutorials, guides etc.
API documentation mostly generated with autodoc.
Documentation directed at developers of your project.
Use this for your change log, license etc.