You want to move AD-integrated zones into an application partition.
Open the DNS Management snap-in.
If an entry for the DNS server you want to connect to does not exist, right-click on DNS in the left pane and select Connect to DNS Server. Select This computer or The following computer, enter the server you want to connect to (if applicable), and click OK.
Expand the server in the left pane and expand either Forward Lookup Zones or Reverse Lookup Zones depending on the type of zone.
Click on the name of the zone.
Right-click on the zone and select Properties.
Click on the Change button beside Replication.
Select the application partition you want to move the zone into.
Click OK twice.
The following command will move a zone to the default application partition that replicates across all domain controllers that are DNS servers in the domain:
> dnscmd <DNSServerName> /zonechangedirectorypartition <ZoneName> /domain
At the time of publication of this book, the DNS WMI Provider did not support programmatically moving a zone into an application partition.
With Windows 2000 Active Directory, if you had AD-integrated zones, those zones were replicated to every domain controller in the domain where they were stored. In many cases, not every domain controller also serves as a DNS server, which results in increased and unnecessary traffic to replicate changes with the zone(s).
Windows Server 2003 provides an elegant solution to this issue by using application partitions. Application partitions are user-defined partitions that can be configured to replicate with any domain controller in a forest. This provides a lot more flexibility for how you store and replicate your AD-integrated zones. You could, in fact, have a couple domain controllers from each domain act as DNS servers for all of your AD domains.
Chapter 17 for more information on application partitions