You can do this simply by installing a Windows Server 2003 domain controller and allowing the schema changes to replicate. Then if you plan on replacing all of the Windows 2000 Server domain controllers, install additional Windows Server 2003 domain controllers. Before you start decommissioning Windows 2000 domain controllers, make sure that the five FSMO roles have been transferred to Windows Server 2003 domain controllers. Don’t forget to configure at least two global catalog server per site, though if the user load is less than 100 or so in remote sites, then it isn’t absolutely necessary.
Once is all said and done and all Windows 2000 domain controllers have been removed, you can raise the domain and forest functional levels to Windows 2003 respectively.
This does not address compatibility issues with other applications such as Exchange Server 5.5 and 200x. You will need to ensure that there aren’t any applications (think: legacy) that depend on the Windows 2000 domain controllers or that will not work propelry with Windows Server 2003. It also does not factor in file and print servers or other network services that must be transferred, such as DHCP, DNS, WINS and so on. These all require attention and proper planning to ensure that there is no, or at least minimal disruption to the user community.
If you have additional questions or concerns, let me and the rest of us know!