Hi Mark
It's difficult in these forums to gauge levels of knowledge and you don't want to end up telling other people "how to suck eggs", (is that just an Aussie saying?), but I'll talk a little about your line ...
"Should the IS, MB's, DB's all be done in seperate jobs?"
Wearing my "backup" hat, the most important thing for our business isn't my ability to recover an individual message for someone. Rather, if our Exchange server and storage is destroyed, we want to get back an ENTIRE mail system, at a relatively recent point in time, quickly.
That said, remember that the Exchange IS is divided into 1 or more Storage Group(s) and each Storage Group contains 1 or more Store(s) and the Public Folder Store.
Also remember that each STORAGE GROUP has its own transaction logs.
The important thing about the BE Exchange agent is that it has direct hooks into Exchange. When an entire Storage Group is successfully backed up, BE signals Exchange to FLUSH the transaction logs and start over for a 'new day'.
If you look back to MY 'personal'/business reason for mail backup, this is the "clean" copy I want in case of a disaster.
So, in a separate job, the FIRST thing I do is back up the entire IS (and the other related bits on the server - Shadow Copy Comonents, Utility Paritition, etc.). I want this over and done with, cleanly, every time. NOTE - you do NOT back up the Exchange databases (*.edb and *.stm files) as "files" - ever - selecting the IS in the backup selection list does this for you.
Once my store backup is done, my jobs then move on to "file share" backups.
Now, what about individual mailboxes? Well, this is really business driven. We don't do it at all. Other users in this forum have written in the past about how their managers insist on it. Microsoft, in Exchange 2K3, recommend it not be done. 2K3 provided the Storage Recovery Group - sure, you have to recover a whole store and then use Exmerge to get out a mailbox, but we just don't have to do it that often, if ever, and so we decided to skip mailbox backups.
If you decide to do mailbox backups, be sure to read the Admin Guide about maiboxes to exclude from backup.
A final hint: refer back to that "flushing transaction logs". Check on your Exchange server, where a particular Storage Group is set to write its transaction logs. If the IS backup has finished cleanly, you will find that there are no logs there older than when that backup started. THERE ARE 2 EXCEPTIONS: "res1.log" & "res2.log"; these 2 files are 'special' and should not be touched.
I hope this helps.
Cheers