I am not really up-to-speed with the changes in 2003 -> 2008 Server domain controllers, I have a mix of both 2003 R2 & 2008 R2, how do I determine which server holds the schema master and must be backed up... I only have one Domain Controller Backup Exec license and know that there is a Primary somewhere....
Really all of your Domain Controllers need to be backed up because if you have a DC that falls out of replication you can lose data that was added to this DC. What you should do is backup all DCs. You can do a simple System State backup and keep it on a network drive some where.
http://technet.microsoft.com/en-us/library/cc755631%28WS.10%29.aspx
Preece