The configuration directory is:
Code:
~/.config/calibre/ # Linux
%APPDATA%\calibre\ # Windows
If you copy it over, it should work more or less. One thing that will definitely break is the library locations, you will need to re-add them.
Installing the official binaries vs. the repository version will not interfere with your configuration!
The error message seems to imply that calibre cannot write a new file to the containing directory:
Code:
/media/username/xxxxxx/Calibre Libraries/Calibre Master Fiction/
Directories have write permissions too.
To fix permission issues with a shotgun

use:
Code:
sudo chmod -R 644 /media/username/xxxxxx/Calibre Libraries/
sudo chmod -R a+X /media/username/xxxxxx/Calibre Libraries/
sudo chown -R username:username /media/username/xxxxxx/Calibre Libraries/