Uninstall the version from the repositories, then install the binary installer from the calibre website. If you have both installed at the same time... well, they try to own the same files.
e.g. /usr/bin/calibre*
As for your library, the library and config data are not touched except when you run calibre. And switching from distro calibre to binary calibre will NOT harm your files anyway.
And just in case you are interested in keeping calibre up to date, see:
Fully automatic calibre installer/updater for linux
Disclaimer: I wrote it, so of course I am biased.
But I really do think it is a must-have.