**** Disclaimer -- works for me, YMMV *****

Steps used to generate a register.com cert
Note: apache/modssl cert

# If necessary login to the GUI as server admin and enable SSL for the site.

   CAUTION: if this site has a cert, and you are renewing do this first save files
   cd /home/sites/host.domain.tld/certs
   mkdir certs_`date -I`.save  (certs_yyyy-mm-dd.save)
   mv * certs_yyyy-mm-dd.save
   
 # login to the GUI as the siteadmin for the site..
   Generate a self-signed-cert.
   This will update the GUI SSL information with dates and years.

 # from the command line, cd to the certs directory and remove those files
   cd /home/sites/host.domain.tld/certs
   rm * 
   You should still have the save directory with the original files if renewal

 # create the 2048 bit csr using this command
   openssl req -new -newkey rsa:2048 -keyout key -nodes -out request
   save these files (key and request) key is very important as it has to match the certificate
   mkdir certs_`date -I`.new  (certs_yyyy-mm-dd.new)
   mv * certs_yyyy-mm-dd.new
 
 # if renewal do the following to return your current cert to proper place
   mv certs_certs_yyyy-mm-dd.save/* .

 # If the customer is purchasing the cert email the customer the csr file 
   contents from "request" file, Or insert at website of cert provider

 # customer or cert provider emailed the files to me which are:
   certificate.crt 
   intermediary_certificate_2.crt 
   intermediary_certificate_1.crt 
   root_certificate.crt (that is the root certificate

 # copy (ftp) certificate.crt to /home/sites/host.domain.tld/certs/certificate
   you need to use the key from certs_yyyy-mm-dd.new
   cp certs_certs_yyyy-mm-dd.new/key .
   
 # There are 3 distinct certs
   intermediary_certificate_2.crt 
   intermediary_certificate_1.crt 
   root_certificate.crt 

 # From the site admin area click-on "Manage Certificate Authorities" 
   Remove any ca's that are there in the GUI 
   Add "Certificate Authority name" browse for file intermediary_certificate_2.crt
   on your PC.
   The same for intermediary_certificate_2.crt and root_certificate.crt.

   check the ca-certs file
   should look like
   -----BEGIN CERTIFICATE-----
     (Your Intermediate certificate 2: intermediary_certificate_2.crt)
   -----END CERTIFICATE-----
   -----BEGIN CERTIFICATE-----
     (Your Intermediate certificate 1: intermediary_certificate_1.crt)
   -----END CERTIFICATE-----
   -----BEGIN CERTIFICATE-----
     (Your Root certificate: root_certificate.crt)
   -----END CERTIFICATE-----

# Restart httpd; 
   /etc/init.d/httpd restart