Okay. Here’s the thing, Calibre creates its own copies of your books when they are added to it. Though that bothers some people it is part of the beauty of Calibre in my opinion.
I maintain a backup of the Calibre library and also store my original copies of my books (in whichever format I purchased it) as well as a cleaned up ePub version once I’ve converted it in Calibre in my own folder which I call Digital Library (because I have no imagination when it comes to naming stuff

)
So you have two choices. If you decide you want to keep your original folder(s)/file system (which is what I would recommend as it can serve as an extra backup) then add all of your books to Calibre and leave your files alone. Otherwise you have the option to delete your folder(s)/files once they’ve been added to Calibre.
1) Create a folder on the external hard drive with the name you wish to call your Calibre library. (“Calibre Library” is the default name but you can call it whatever you want)
2) Open Calibre and click on the Calibre library icon on the toolbar (see attached image)
3) Select the “Switch/create library” option
4) The
Choose your calibre library pop-up window will appear which will show the current path of your library (see image attached).
5) Click on the little window icon to the right of the “New Location” field and select the folder you created on your external hard drive.
6) If there are books in Calibre already you wish to keep, select the “Move current library to new location” option. If you want to start fresh or have no books currently in Calibre choose the “Create an empty library at the new location”
7) Once you have your pathway and options selected, click OK
8) This is now where Calibre will store its copies of your books.
Now to add your books to Calibre:
Here is a link to the GUI instructions on Calibre’s website
http://manual.calibre-ebook.com/gui.html#add-books
So you can either instruct Calibre to add of your books or do so yourself manually. Click on the down arrow ˇon the right of the “Add books” icon (see attached photo) and choose the option that best suits your needs. You can always change the default folder to add books from once you have added your current collection. I have a folder in My Documents called “TEMP for Calibre” (see no imagination

) that I store my books in temporarily until they’ve been added to Calibre.
There are ways to automate the adding of books, but I would leave that until you get the ones you already own all set up.
Also, the initial set-up/adding books to Calibre is the toughest part. Once you have your library set up, adding your new purchases however often you wish to do so is much simpler.
Once you have your books added into your library you can clean up the metadata, ensure your author names display the way you want them to, etc.
If you haven’t already watched them, Kovid has some video tutorials on the Calibre website, too which are helpful
http://calibre-ebook.com/demo#tutorials
If you need any help, just ask.