For the most part configuring certificate auto-enrollment is a fairly straight forward process, and is well documented (see links below).
http://www.microsoft.com/technet/prodtechnol/windowsserver2003/technologies/security/autoenro.mspx
http://www.microsoft.com/technet/prodtechnol/windowsserver2003/technologies/security/ws03crtm.mspx
Nevertheless, there is one aspect that may not be quite intuitive and it has to do with the certificate templates versions. As you probably are aware Microsoft Enterprise CA supports two types of templates: V1 and V2. V2 templates allow customization and therefore are preferred, but require CA to be running on Windows 2003 Server Enterprise Edition. So where is the non-intuitive part? Well, the auto-enrollment configuration process will differ depending on the type of the template the certificate is based on.
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