"Upgrading" from 2003 server to 2008 server is probably not possible anyway. Most 2003 servers were installed in 32bit., while "2008 r2" (Windows 7 based) server only comes as 64bit. Also if you only use the "2008" (Vista based) server which comes as either 32 or 64 bit, you'd have to choose the correct one.
Upgrades only work inside the same bit level:
Windows 2003 32bit to Windows 2008 32bit
or
Windows 2003 64bit to Windows 2008 64bit or 2008 r2
So it is very likely that rather than an upgrade, you'll have to do a fresh installation. Besides, from 2008 server upwards, the directory structure is different from previous OS's...
Ok, so there should be backup ./ restore to keep the data from previous versions
rindi
If it's the only DC in your environment, that isn't enough. If you want to keep any Active Directory info, you must install the new OS separately, then add it to the Domain and promote it to a DC. That will pull in all AD data. Then add the FSMO roles to the new server. After that the old server can be shutdown.