Folders in GoodNotes are like those you know from your computer. They can contain as many documents and other folders as you need for your organizing purposes.
To start creating a folder, tap on the large + button in the Documents tab of the library, and choose "Folder."
To create a folder inside another, open the containing folder, tap the "+" icon, then "Folder" like above.
This way, you can create a system of organization for all your documents in GoodNotes.
See also: Creating a notebook in GoodNotes 5