Edit /etc/courier/imapd-ssl and change the values of TLS_CERTFILE and TLS_TRUSTCERTS to

TLS_CERTFILE=/etc/ssl/self-signed/server.pem
TLS_TRUSTCERTS=/etc/ssl/self-signed/server.crt

To restart Courier you have to restart couple of services.

/etc/init.d/courier-authdaemon restart
/etc/init.d/courier-imap restart
/etc/init.d/courier-imap-ssl restart

And if you have it installed POP3 you need to restart those as well.

/etc/init.d/courier-pop restart
/etc/init.d/courier-pop-ssl restart

If you would like users of every virtual domain on your server to connect to mail.their-domain.com instead of to atlantis.example.com you will have to sign new certificates for every domain and also use a separate IP address for each virtual host. Information on placing certificates for various hosts can be found in /etc/courier/imapd-ssl.