There's a lot of confusion going on here; terminologies being used to refer to things other than what they actually mean, so let's first put things into perspective so that we all understand exactly what is being referred to when a term is used.
The user profile directory aka home directory, C:\Users\<username> contains special user data folders namely My Documents, My Music, My Videos, collectively known as user shell folders or user profile folders. These are system-generated when you log into a new user account for the first time. They are not ordinary folders because they do not really contain data and instead, they are virtual folders that link to locations where the data is actually stored. As you've discovered, the locations that these shell folders link to are configurable (can be changed), the same way you can change the target of a shortcut. Shell folders and their target locations are defined in the Registry, so when you move their contents to a custom location as described in this tutorial, their registry entries are also modified to reflect those changes.
Libraries on the other hand are NOT folders. There's a tendency to wrongly refer to shell folders as "libraries", but they are NOT libraries. Libraries are not folders and folders are not libraries. They are entirely different objects. Libraries DO NOT store/contain files like folders do. Libraries are simply views. They give you a singular viewpoint from which you can access files stored in different locations. In other words, libraries are just views of indexed data, much like a card index in a physical library. They simply point you to contents stored in different locations. You can read more about Libraries here https://technet.microsoft.com/en-us/library/ee449413(v=ws.10).aspx, that FAQ article explains better than I can.
You cannot redirect Libraries to some other location, like that PCWorld article claims. However, you can redirect the user shell folders to a location of your choosing. You can do this via the Registry (not recommended for novices) or use the location tab of their properties dialog (highly recommended). You can add additional locations to an existing library or create additional libraries.
What you were seeking to do is redirect your user shell folders, and NOT libraries, to a custom location (different partition), and in so doing you accidentally redirected the My Music and My Documents shell folders to the same location, and in attempting to rectify your mistake and start over you deleted those two shell folders. When you tried to create the My Documents folder, a duplicate one was found, but you couldn't see it even if you confirmed the prompt to merge the two together. This is where things can get really confusing. There is a folder junction called My Documents and it's super hidden (a protected operating system file). It is not visible until you enable the display of hidden, system-protected files. Whatever you do, DO NOT touch this junction.
Another major point of confusion is how Windows Explorer or the shell presents the user shell folders. The path of the default location of the My Documents shell folder is C:\Users\<username>\Documents, yet if you were to open the same location, what you see is My Documents (in Windows 7). Explorer presents My Documents (it's what you see), yet the default location does not have "My" in its path. If you tried to open C:\Users\<username>\My Documents from the Run dialog, you'll get an access denied message or a message saying that location could not be found, yet if you typed in C:\Users\<username>\Documents it opens the My Documents location! Alternatively, if you changed to C:\Users\<username>\My Documents in CMD, it has no problem getting in! By default, the My Documents junction is owned by SYSTEM and It is super hidden and restricted for good measure, so I cannot emphasize enough why this junction should be left alone. In fact, you shouldn't even enable visibility of hidden and system protected files and folders. You have no reason to, even if to revert the mess you're in right now.
Enough of all that, let's restore the two user shell folders you deleted. Follow this tutorial and let's know how it goes.
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whatever you decide, ensure you have restorable weekly-made or bi-monthly-made full images of your OS and data partitions.
