[itimpi]

Using Dropbox with Calibre is certainly not mandated, but many people find it convenient. You do, however, need to be aware of the space your library will use and the space you have available on your Dropbox account when using this approach. This may make Dropbox impractical for those with very large ebook libraries (mine for example is about 40GB and thus too large for my Dropbox account).

The calibre library in Dropbox will contain copies of all the books you have added to Calibre. If you also have copies in your Dropbox folder outside the Calibre library then these can be removed from Dropbox to avoid duplication.

I am assuming that you have not put the Calibre library at the top level of the Dropbox folder as that would get messy? I would expect the Calibre library to be in a folder of its own (e.g. "My calibre Library"). Everything inside that folder is then under the control of Calibre and should not be manipulated outside Calibre. There will be additional files for purposes of metadata, cover, etc but you should not need to worry about these.