Thanks to all the origninal poster, please visit each link:
Install and configure an Enterprise Root CA
http://technet.microsoft.com/en-us/library/cc731183.aspx
http://www.vkernel.ro/blog/install-certification-authority-in-windows-server-2008-r2
Install and configure a Subordiante CA:
http://technet.microsoft.com/en-us/library/cc772192.aspx
One of the best Complete guide I have found.
http://marckean.wordpress.com/2010/07/28/build-an-offline-root-ca-with-a-subordinate-ca/