The X.509 private key and certificate need to be configured on the server end. They can be specified using the -x509cert and -x509key options to vncserver or the equivalent turbovncserver.conf variables. If unspecified, vncserver will try to use ~/.vnc/x509_cert.pem and ~/.vnc/x509_key.pem, if they exist. The X.509 CA cert and CRL in the TurboVNC Viewer are only necessary if you self-signed your certificate or used a certificate authority whose root certificate is unknown to Java. Even then, I have never found that I needed to specify the CRL with self-signed certificates— just the CA cert.
In windows TurboVNC v3.0.2 there are setting for secur connections using certificates.