How to forward DNS queries for specific domain to a specific DNS server.
This goal can be achieved using Conditional forwarding that is supported in Windows Server 2003 and Windows Server 2008.
Configure Conditional Forwarding on Windows Server 2003 or Windows Server 2008 DNS Server
1. Open Server Manager, expend to DNS under roles ( on Server 2003 open DNS console)
2. Right Click on the DNS Server and choose “Properties”
3. On “Forwarders” tab, click “New”
4. Enter the domain name and press OK
5. In DNS Domain box, Click the domain name and add list of DNS server,
6. Then Click Apply or OK
As you can see, this will help you control DNS queries for specific domain to a specific DNS server.