How to back up Backup Exec system databases (master, model, msdb):
Backup Exec system databases can be backed up by the following backup job when you have a valid license for "Agent for Applications and Databases:"
1. Open the Backup Exec console.
2. Create a full backup job. (See Fig 1)
Fig 1

3. Check Microsoft SQL Server Instances > BKUPEXEC. (See Fig 2)
Fig 2

4. Uncheck Use snapshot technology under the Advanced Open File dialogue. (See Fig 3)
Fig 3

5. Run the backup job.
6. Open Explorer and browse to the SQL install path after the backup job completes
The default SQL install path:
Backup Exec 21.x: C:\Program Files\Microsoft SQL Server\MSSQL12.BKUPEXEC\MSSQL\DATA
Backup Exec 22 or later: C:\Program Files\Microsoft SQL Server\MSSQL14.BKUPEXEC64\MSSQL\DATA
Note: The backup job can be deleted after completion if you do not plan to run it periodically.
How to back up Backup Exec database (BEDB):
The Backup Exec database (BEDB) is automatically backed up every day at 4:00 AM by default. In general, manual backup is not required.
If you would like to manually back up Backup Exec database (BEDB), please back it up by the following operations:
1. Open Explorer. Browse to the Backup Exec install path.
The default Backup Exec install path:
C:\Program Files\Veritas\Backup Exec\BEUtility.exe
2. Run BEUtility.exe. Click Yes in a popup message.
3. Click All Backup Exec Servers. Right-click your server name.
4. Select Dump Database. Click Yes if a popup message appears.
5. Click Close after Progress reaches 100%.
6. Open Explorer. Browse to BEDB.bak in the Data folder of the Backup Exec install path.
The default Backup Exec install path:
Backup Exec 16: C:\Program Files\Veritas\Backup Exec\Data\BEDB.bak
7. Confirm the time stamp for BEDB.bak has been updated.
Note: Databases can be backed up as a flat-file by a full backup job when you do not have the license for "Agent for Applications and Databases".