No idea how Microsoft internal tools interacts with the service. You'd have to ask them, and they won't tell you. A friend used to work in MSIT building said tools, and even he wouldn't tell me.
However, there should be a sample in the Windows SDK that gets installed here (source: http://blogs.msdn.com/b/alejacma/archive/2010/10/08/how-to-access-the-new-certificate-enrollment-web-services-programmatically.aspxLink):
C:\Program Files\Microsoft SDKs\Windows\v7.1\Samples\security\x509 certificate enrollment\CSharp\enrollWithIX509EnrollmentHelper
According to various sources its not the most in depth sample, so see here too: http://blogs.msdn.com/b/alejacma/archive/2011/11/07/how-to-request-a-certificate-programmatically-using-the-certificate-enrollment-web-services-c.aspxLink