Magic phrase
Command line interface Start one for EACH.Assign a different PORT for Each

Avoid the port assigned to the GUI version (eg 8080), just in case it gets started. (I don't ust that one as it follows which Library I am viewing)
Code:
"C:\Program Files\Calibre2\calibre-server.exe" --port 8083 --with-library C:\Users\ME\MainLib
"C:\Program Files\Calibre2\calibre-server.exe" --port 8082 --with-library C:\Users\Me\JuivLib