You should have at least three "Library" folders. One is inside the System folder and supports system-level stuff that you as a day-to-day user don't normally need to deal with. Another one is in the top level, directly under the hard drive. This supports things that are common to all users, like support for applications. The third one is in your user folder, and this supports things that are unique to you as a user, like preferences and settings.
Edit: Those are just the main ones...Spotlight actually pulls up eleven separate folders named either "Library" or "library" on my system. You can always control-click or right click on a Spotlight result and choose "Reveal in Finder" to figure out where the file/folder exists.