Hello,
You should be able to restore the files. However we recommend creating separate backup jobs for SQL and other normal files. Please do not backup the Backup Exec's MSDE instance. This is not required. Backup Exec will automatically back it up.
When you create backup jobs, do not use AOFO for SQL backups. For other files you may use AOFO.
Please refer the following technote which gives detailed information on the AOFO option and its usage.
Title:
What is the intended use of the Open File Option and the Advanced Open File Option?
http://support.veritas.com/docs/263784
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