The simplest solution is to move the Calibre library to the updog folder and use Calibre2opds in its default mode to generate the catalog as a sub-folder (default name of '_catalog') of the Calibre library folder. In this scenario it is recommended that you turn of Dropbox sync while running Calibre to update your library, although in practise you will probably get away without doing this if you never run Calibre on another machine at the same time.
The alternative is to have the Calibre library folder somewhere else and run Calibre2opds in its 'publish' mode to create a a copy of the Calibre library and Calibre2opds catalog in the updog library folder under DropBox. This would mean that you end up with a second copy of your Calibre library - one in the current location and the other in the updog folder under Dropbox. This scenario avoids any potential DropBox sync issues as your master Calibre library is no longer under DropBox control.
Both the above scenarios have been used while testing Calibre2opds with the updog+DropBox combination . I will update the Calibre2opds documentation to try and make the options clearer.
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