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Your calibre library is the 'My Documents/Calibre ebooks' directory. When importing calibre will store the books there. The entire library consists of the book files, covers, and the metadata.db file. Leave the library alone and do not touch anything in it outside of calibre.
'Save to disk' is exactly what it says it saves the file to disk. calibre stores the ebook files in the library but the metadata is stored separately in the metadata.db file. When you use 'Save to disk' it will save the file in your requested location and update the metadata on that file.
'Save to disk' is necessary for instances when calibre doesn't support a particular reader because it still allows you to save books onto it. Also, it allows you to back up your collection without backing up the actual library (just the ebooks with the correct metadata). It is also handy if you want to put a book on say a thumb drive to share with a friend.
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