Which service are you trying to setup with the certificate?
There is a guide here:
For example for Apache you can set apache2/ssl/certificate and apache2/ssl/key to the purchased cert to use it for web related access. For dovecot the same is mail/dovecot/ssl/certificate and mail/dovecot/ssl/key .
If the certificate contains a complete chain, you should be able to put all intermediate certs in one file and provide that.
UCS also uses certificates for internal communication, IMO it is not advisable to try to replace those certificates.