I'll answer your points in order:
1.It seems you also have some confusion over the way BackupExec does full backups of SQL Server.
To perform a full backup, two separate jobs are needed:
a. Full backup of the database
b. Full backup of the transaction logs.
It would seem to make sense to have a backup option that carried out both steps. In fact, for Exchange Server (which has a similar storage method), you have exactly that - an option to do a full backup including logs.
2. Pointless response, irrelevant to my question. I assume you're talking about running a backup via SQL Enterprise Manager. Not interested, it can be done with BackupExec, it's just a pain.
3. Not using AOFO, was not mentioned in my message, irrelevant.
4. I'm aware the truncation is done by SQL, my point is that you need to run two different types of full backup in BackupExec before it signals to SQL that the logs can be cleared.
5. I'm using SQL 2000 and running weekly full backups with daily differentials. This means I run:
Weekly full backup job 1 - full backup of databases
Weekly full backup job 2 - full backup of logs
Daily differential backup - full backup of logs (no truncate)