Do a little searching on the web, and you will find all sorts having problem updating the domain controllers from one version of Windows to the other .... humm, I have had some issues, and the issues stem from a bit of a confusion. Microsoft is not guiltless here since they sort of do the chicken and egg thing - you need to do this first, but you don't have it to do it.
The utility you need is adprep. The main thing you want to keep in mind is that you need the adprep that fits your environment. For example - You have Windows 2003 32 Domain controller, so in order to upgrade to Windows 2008 whatever (including 64 bit R2), you need the adprep from Windows 2008 32 bit, not 64 bit and not R2 either. So the confusion would be that if you are trying to put in a Windows 2008 64 bit Domain controller in a Windows 2003 32, you need to find the right adprep.
Now, where to find the right adprep. The utility seems to be in different location with different versions. In the R2 the adprep is in the second DVD in the "sources" folder, but in the single DVD 32 version of 2008 it is in CMPNENTS.
Seems like Microsoft could simplify the process by making sure that the right adprep is in all the DVDs and just label the folder accordingly because it can be that a person trying to the an upgrade is stuck searching the internet for it or downloading and ISO just to get the right version.
Important: Since at the time of running ADPREP you still do not have any Windows Server 2008 Domain Controllers, it should be made clear that these commands MUST be run on EXISTING Windows 2000 or Windows Server 2003 Domain Controllers. That is why you MUST make sure you keep a copy of the 32-bit version of the Windows Server 2008 installation DVD. You cannot use the 64-bit version of the installation media to run ADPREP on 32-bit versions of Windows 2000/2003. Because Windows Server 2008 installation media is 64-bit by default, remember to request the 32-bit version when you get your copy. In case you don't have the 32-bit version available, you can also use the evaluation version of Windows Server 2008 32-bit installation media to run ADPREP, so just download the file from Microsoft's website, and use it to run ADPREP on your 32-bit Windows 2000/2003 DCs.