If you're installing Windows 2003 R2 on an existing Windows 2003 server with SP1 installed, you require only the second R2 CD-ROM. Insert the second CD and the r2auto.exe will display the Windows 2003 R2 Continue Setup screen.
If you're installing R2 on a domain controller (DC), you must first upgrade the schema to the R2 version (this is a minor change and mostly related to the new Dfs replication engine). To update the schema, run the Adprep utility, which you'll find in the Cmpnents\r2\adprep folder on the second CD-ROM. Before running this command, ensure all DCs are running Windows 2003 or Windows 2000 with SP2 (or later).