You can configure the passphrases that a listener requires in the mf-server.dat file. When you start the listener, it retrieves the passphrases from the file, and you do not need to configure them manually.
The mf-server.dat file is in the %ProgramFiles(x86)%\Micro Focus\Visual COBOL for Visual Studio 2013\bin or \bin64 directory by default.
[Listener-name/SSL/passphrases] certificate=certificate passphrase keyfile=keyfile passphrasewhere: