Documents, folders, and top-level Rems are often confused. While they may appear similar at first glance, they have distinct meanings and functions, and any particular Rem can be a document, a top-level Rem, both, or neither.
First of all, there is no fundamental difference between folders and documents; a folder is just a document that contains other documents, and a Rem being considered a folder rather than a document has no effect beyond changing the icon that appears next to it.
What about documents and top-level Rems?
You can mark any Rem at all as a document, for instance by typing
/documentor pressing Ctrl+Alt+Shift+D (Cmd+Opt+Shift+D on a Mac). This has several effects which you can read about in the documents article. The main purpose of marking something as a document is to indicate that this is usually the level that you'll want to zoom into when working with the contents of that document. But if a document has parents, you can zoom out further, or you can zoom in to a child Rem of the document.
Most people create a document for each lecture or article they take notes on, or each low-level topic they want to write or think about, then organize these documents into larger folders like “Chemistry” or “Programming Languages” or “Cities.”
Here are some examples of documents that are not top-level Rems, using a knowledge base hierarchy based on the Johnny Decimal System (you can see the hierarchy of folders underneath each document name in bold):
A top-level Rem is any Rem that doesn't have a parent. Often, top-level Rems will be marked as documents, but they don't have to be. For instance, if you create a new top-level Rem by pressing Ctrl+Enter in reference, tag, or global search, it won't be a document.
Many people like to create top-level Rems for named concepts or ideas that come up in a document they're writing but that they don't yet have much information about. If you do this routinely, you'll be able to see everywhere you referred to each concept through backlinks, and you'll have a place ready to put more information about it if you need it later.
It can also be useful to hoist concepts that appear in multiple documents and sources into top-level Rems and then display them in each document through a portal.
Here are some examples of top-level Rems that aren't documents: