I use the following process to create certs on my SCS system:
Log on to the machine that SCS is installed on . Open a web browser on that system and enter the url of the machine issuing certs for your domain followed by certsrv. It will look something like this: http://192.168.1.1/certsrv
Login as the domain admin.
Click on Request a certificate.
Click on "Advanced certificate request".
Click on "Create and submit a request to this CA."
In the certificate template field, select the template that you built.
You will then be able to specify the subject name equal to the machine name.
Once the template is in place - when you request the certificate, the "first name" is the FQDN of the target system used for remote configuration.
I'm planning to put together a short video to show how this is done... hopefully have it posted before end of the month...
Thank you for the help. From your replies, I was able to figure out my problem. When I built the template for the cert I forgot to select the "Supply in the Request" radio button. When AD fills in the data, it want to use the user name rather than the machine name. When I changed the template to function this whay, then it worked exactly as I needed it to. It would be helpful if this was noted in the section on generating a remote config cert.