You must take these steps to add an X.509 certificate from another CA:
1) Have the user install the certificate in his/her browser
2) Have the user open the certca.nsf database on your Domino server using SSL (use a URL with https://)
3) Have the user choose "Register Client Certificate"
4) The Domino administrator then has to open certca.nsf in the notes client and validate the request. This transfers processing of the request to the AdminP process which has to be running properly.
5) The Domino administrator can then wait for AdminP to process the request on its normal schedule or tell it to process the request immediate as documented in the Notes Help.