If your DNS server is running Windows Server Core, you can configure conditional forwarders on your DNS server from the command-line by using the DNSCMD command. A conditional forwarder is a forwarder that handles queries only for a specified domain name. Conditional forwarding enables a DNS server to forward queries for different domain names to different DNS servers according to the specific domain names that are contained in the queries. This improves conventional forwarding by adding a second condition to the forwarding process. To configure a conditional forwarder, you specify a domain and one or more IP addresses of DNS servers that can resolve queries directed to that domain.
You can use Dnscmd to configure conditional forwarders for your DNS server. For example, to configure a conditional forwarder that forwards all queries for hosts in the microsoft.com domain to the external DNS server 126.96.36.199, do the following:
dnscmd SEA-SC4 /zoneadd microsoft.com /forwarder 188.8.131.52
If your DNS server is on a domain controller, use /dsforwarder instead of /forwarder in this command.
For more information on managing DNS servers running on Windows Server Core, see my book Windows Server 2008 Server Core Administrator's Pocket Consultant from Microsoft Press.