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