There are two Library folders /Library (the system one) and ~/Library (the user one for your account). If you've accidentally moved the user one from your home directory, ignore the one in the root as it's where it's meant to be.
Use the Finder's Find... option from the File menu. Select Kind as folders and type Library into the search box. You should get two Library folders in the results. Select each to reveal the path to them in the window. The one not directly under Macintosh HD is the one you need to move back to your home directory.