For a backup of BE server itself, you do not need to backup SQL. BE automatically backs up the SQL DB as part of a daily maintenance. You need to backup only the regular file data such as C:\, System State etc.
...BE will backup bedb.bak to be precise. Unless you have the SQL agent installed, it won't touch SQL and will in fact exclude the *.ldf and *.mdf files.
...for installed files you can select R:\, and Backup Exec will exclude the *.mdf and *.ldf files through Active File Exclusion. The selection in your post above is fine.
If you are only looking at the BEDB instance and not another application running in SQL then you could schedule the BEDB maintenance for 10 minutes before the backup job starts and then just backup the BEDB.bak file from the data folder and not actually do a SQL backup of the BEDB (which would then mean you are not using the SQL Agent and therefore do not need an Application and Databases license).
Note: A standard Backup Exec Server license does not include the applications and databases license so you would need to add such a license to backup the BEDB if you continue to back it up via the SQL selections (you might be in trial/evaluauon mode for 60 days)
