It is not a god idea to use a Windows calibre library on a linux OS. Windows is case-insensitive, as is the db. Linux is case-sensitive and will not be able to find your books. You should be able to reemotely access calibre on the server, though:
http://courses.cms.caltech.edu/cs11/misc/xwindows.html
You can run as many instances of
Code:
calibre-server --port #### --with-library /path/to/library
as you want.
Just make sure they broadcast on different ports.
You could also merge the libraries and separate them via
virtual libraries, which can be searched in the server.