Publish root CA and sub ca certificate to the Trusted root certificate store
There are two methods. You can either use Group Policy to distribute the certificates to domain clients, or you can use certutil.exe -dspublish -f <certfilename> RootCA. There are advantages to either method. The dspublish method is simpler, but the Group Policy method is a bit more flexible. Using Group Policy, you can scope the recipients of the certificate(s) to certain OUs, configure extended properties like Extended Validation, OCSP responders, etc.
http://technet.microsoft.com/en-us/library/cc782744(v=WS.10).aspx
OR
But you do not need to do both.