The change from a windows 2000 active directory domain to a windows 2003 active directory domain is large enough that I would recommend new material. A lot of the Microsoft study material for 2003 will actually point out how things were done on older systems compared to how they are done now. This helps you learn both systems.
More importantly I would say the move to server 2008 from 2003 is an even bigger change. Although most networks still run primarily on 2003 software eventually everyone will have to migrate. My recommendation would be to go get study material for 2008 and get hands on experience will all of the above using virtual machines.