If you are trying to backup the media server then please be aware that you may need to understand the difference Between "Media Inventory" and the backup set "Catalogs" - especially as you probably need to backup both of them.
Although this document is written to explain something to avoid doing, it does describe the key components of Backup Exec which should help you understand the terms and concepts
http://www.symantec.com/docs/TECH176061
At a basic level, the recommendation would be backup the catalogs files when no other jiobs are running, and just before you do this backup also dump the BEDB and back that up in the same backup. This will give you the most consistent view of you data should you have to recover it
Note: because of how the document was written it does not mention that the BEDB also contains your job configurations however, backing up in the way described will retain these as well.
If you need to backup your job logs as well, then backup the .xml files in the data directory as well as the BEDB and the catalogs folder.
