The R2 ADPREP must be run on the 2000 DC.
Here are some related links:
Here are some links that should get you going for upgrading a 2000 domain to 2003:
Common Mistakes When Upgrading a Windows 2000 Domain To a Windows 2003 Domain
Hotfixes to install before you run adprep /Forestprep on a Windows 2000 domain controller to prepare the Forest and domains for the addition of Windows Server 2003-based domain controllers
Commodore.ca | Windows | How To Upgrade Windows 2000 Domain to Windows 2003 Server
Quote from the top of this article: "Several glossy Microsoft presenters have stated that all you need to do to complete a Windows 2003 Domain upgrade is run ADPREP and then upgrade away. This may work for very small / simple environments but it is definitely not good advice for most companies. After upgrading five servers in two unrelated domains and installing many fresh copies of 2003 I can say that I personally would not skip a single step in the process I have developed below."
How can I transfer some or all of the FSMO Roles from one DC to another?
How To Create or Move a Global Catalog in Windows 2000
[If you run Exchange 2000] Windows Server 2003 adprep /forestprep Command Causes Mangled Attributes in Windows 2000 Forests That Contain Exchange 2000 Servers
Windows Server 2003 Upgrade Assistance Center
[If using R2 release of Windows 2003] Extending Your Active Directory Schema for New Features in Windows Server 2003 R2
How to move a DHCP database from a computer that is running Windows NT Server 4.0, Windows 2000, or Windows Server 2003 to a computer that is running Windows Server 2003
How can I move a DHCP database from one server to another?
How can I move DNS from one Windows 2000 Server to another Windows 2000 Server?
(Two Related if going 2000 to 2003 - read both before moving)