A content server instance accesses and serves one library.
If you start the content server from the GUI then the library is the one open or subsequently changed-to in the GUI. If you start the content server from the command line then the library is the one named in --with-library or in the default preferences if --with-library is not specified. You can serve multiple libraries by starting multiple instances of the content server. Use a different port for each server (--port).
Instead of multiple libraries you might consider using restrictions to create virtual libraries. You can specify a restriction when you start the content server, permitting you to emulate any subset of "separate" libraries in one server instance.
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