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/