Two library folders

I was working on a plug-in issue (Aperture) and have come to the realization that I have two library folders for my OS.
The first is in the root directory of my hard disk  [hard_disk]/Library
The second is under the same hard disk, but is then under /users/[username]/Library
In both locations, I have a sub folder called /Application Support/ then various application folders are there.
Am I supposed to have two Library folders, and/or am I supposed to have two /Library/Applications Support folders?   The contents appear to be different in each.
As a note, when I set up this computer, I copied files and folders over from our previous iMac which was running regular Leopard.
Thanks,
Mark

Actually there are three Library folders, and yes they are supposed to be there.  These folders contain similar items, but operate at the different levels of the OS - the /System/Library folder is for system files, the /Library folder is for items that apply to all users, and the /Users/you/Library folder has stuff that only applies to your user account.

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