You can create collections to organize your documents in whatever groupings make sense to you. Documents can be in more than one collection.
To create a new collection, click on the "New Collection" field under "Collections" and begin typing. Once you have created a collection, you can rename it or delete it by right clicking on the collection name in the left hand panel or by clicking on the three dots which appear at the end of the collection name when hovering your mouse over the name.
To add a reference to a collection, drag and drop it onto a collection in the left hand panel, or select multiple references and select "Add to Collection" from the "Organize" menu at the bottom of the screen.