Ok you generated the new CSR after that you have purchased a certificate from a vendor?
Is it a chained certificate (Godaddy and comodo issued chained certificates) if so you will also need the CA bundle.
To install the new certificate you can just install it over the old one, or you can remove the old certificate first.
If you are installing over the old one make sure that you paste the new .key file and the certificate file into the correct boxes, make sure that the IP address and domain are correct, if it is a chained certificate make sure you paste the correct CA bundle file in the bottom box. Then click on Do It.
If you want to remove the old certificate first you can do that by going to SSL/TLS in WHM and selecting Delete SSL Host, this will bring up a list of Hosts with SSL on the server. Click on the required host to remove the certificate. You can then install from Scratch, you will need the .key file that was sent to you in the second email when you generated the CSR as all information will have been removed from the server.