Where should folders be?

I noticed I have a Application Folder and a Library Folder (both with icons on it) directly on my Hard Disk, as well as in my Home (house) folder. They're not all duplicates. This shouldn't be, should it ?
Two questions:
1) Where should these be?
2) Should I let one overwrite the other keeping the latest modified date?
I just installed an application and it was put in the App folder directly on the HD. I presume this is the important one?
Thanks,
Stu

From your Help menu, search for *how your computer is organized*
Also, see
Basic Tutorials on using a Mac,
Mac 101: Mac Essentials,
Mac OS X keyboard shortcuts,
Anatomy of a Mac, and
ont Locations and Their Purposes

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