Hi Jim,
You need to create all the files from scratch if you are replacing the default certificates.
sso.cfg is similar to openssl.cfg which has the details to include in the certificate.
key file and csr file is the output file you get from this command
If you want to create certificate for vcenter 5.1 or 5.5 components, I would suggest to use the SSL automation tool provided by VMware.
It has simple steps to create certificate request by answering the details, it makes the cfg file as well for you to verify the details at a later stage.
use the same tool to apply the certificate as well. benifit is you just need to make one format and supply it to the tools, when you apply certificate the tool has the capability to convert it to the right formats.
Refer KB articles 2057340 to use the automation tool, Also you will get a manual along with the tool.