Our POP/IMAP are not seperate daemons. They are native in our tomcat webapp along with the SOAP service. Actually makes it very nice since IMAP/POP/SOAP can all share the same caches and will never get out of sync. So no matter what client AJAX, Outlook, Thunderbird, Treo, etc connects they will all see the same data and changes right away. Just thouhgt I'd mention that to clear up an misconceptions.
So to install a real cert the commands are here:
certs
Just need to reference your cert rather than the self-signed ones we create.