Yesterday I was tasked with installing new SSL certs on several Linux machines. This environment has a local CA in place on the domain.
I generated a CSR on the server via OpenSSH and copied them to my Windows CA.
To generate the certificate you will need to know which template to use. To view all the templates on the server, run the following command-
In my case, I went with the "Web Server" template To generate the certificate run the following command-
certreq -attrib "CertificateTemplate:WebServer"
After you run this command you can browse to the CSR and then export a SSL certificate.