I think what you are telling me is that you are backing up the SQL DB's and Store using the same backup job. If that is possible then go for it.
Just remember,
EV should either be shutdown or placed in Read-Only mode. R/O mode will allow users to view their items but no modifications can be done. The SQL database in not being populated with new or deleted items. The indexes are not being updated.
The system will be in a fairly consistent state for a backup. Read the backup instructions and backup all areas as indicated.
Admin Guide - Check for EV backup procedures section.
http://seer.entsupport.symantec.com/docs/289858.htm
The index location is mentioned ans should be backed up. If a large index gets corrupt then tech support will advise you to restore from backup then run and update from the GUI against the index. Rebuilding a large index can take a large amount of time and EV resources.
To avoid index corruption make sure you exclude the indexes from being scanned by your AntiVirus. This will also help performance. It is recommended to exclude the MSMQ, Vault Store, and Indexes.
Jim S.