Update SSL over SSH & FTP - ONLY

I want to update SSL with certificates which I already have as part of routine over SSH ONLY so that I can manage fully over SSH. I upload the certificates manually over FTP and then need to do the same functions I can do on the SSL page in cpanel, but do this over SSH ONLY. Please tell me the specific lines to copy and paste in SSH, for example, for the domain mydomain.com (this is not a real domain obviously). All the info needed for this question has already been included above. DELETE SINCE I CANNOT EDIT I HAVE ASKED THE QUESTION AGAIN EDITED. I WILL NOT LOOK HERE AGAIN AND HAVE UNSUBSCRIBED. SEE NEW THREAD.