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Number one: don't touch that library of books, which I'm guessing is what you mean by "Calibre folders" (if it's a heap of folders named by author, and containing sets of files with suffixes like .opf and .jpg and .epub). Leave that library completely as it is.
Where did you copy the app to when you installed it? When you downloaded the dmg file, you should have copied it across to your Applications folder.
If calibre.app is not in Applications, and a Spotlight search of your hard drive doesn't find it, I wonder if you just ran the app from the mounted disk image instead of actually installing it. In which case all you should have to do is re-download the app, and install it properly this time, pointing it to your existing library of books. After installing it in your Applications folder, you can put the icon in your Dock for easy access.
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