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Are there any guides for configuring multiple sub-domains in a single site regarding replication? This scenario is further compounded by the sub-domains being Win2k and Win2k3.
There are no real guides, but the is a lot of information on Active Directory design, from the Windows 2000/2003 resource kit, the MS Training Materials, MS White papers, etc. Generally though you will find the creation of multiple domains is discouraged without true valid purpose. Creation of Organizational Units for administration is much more flexible and far less system-intensive.