Add an option to the lib and app schematics to provide the directory where it will be created. Example:

ng g lib myLib --directory=libs/helpers

ng g lib generalUI --directory=libs/shared-components

This would allow users to create nested folder structures for their libs and apps.

Schematic would need to use the directory value for the file locations and use it in conjunction with the sourceDir when setting the root property of the app in the .angular-cli.json file.