That's right; the base views created on the same level as the data source are meant to be organized into different folders, while the base view under the data source object represents the base views that were created from that data source.
In order to easily access my base views, I usually create a separate folder for them different from the data sources folder. This way, all the database connectivity information is separate from the table information and I can have a folder that contains all of the base level information for a project. Then, while I am creating base views from a database, I can modify the "Folder" attribute in the "Metadata" tab to have the view save to the correct folder.
For more information about the Denodo recommended folder organization and naming conventions, you can refer to the [VDP Naming Conventions](https://community.denodo.com/kb/view/document/VDP%20Naming%20Conventions?category=Operation) page of the Denodo Knowledge Base.
I hope this helps!