You define the hierarchy for your organizational units (OUs) with the organziationalUnits property at the top level of the organization.yml file. It's an object whose keys are OU paths, and values are configuration for the corresponding OUs.
The root OU of the hierarchy is always Root, and all other OUs are its children.
This is the minimum hierarchy. As you can see, you must have the Root OU but you don't have to provide configuration for it.
Here we have a more complex hierarchy with some nested OUs.
The above configuration is flat but represents this kind of hierarchy: