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: Link):
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: Link
