Hey! So, I'm going to assume you got the Backup Exec 12.5 here from TechSoup - which basically covers unlimited agents and licenses (unless I'm mistaken). The one piece of software missing from BE12.5 (at least from the description) appears to be Vista, so if you need to back up a Vista machine for any reason and it doesn't have an agent available, let me know and I'll help you with a strategy for that.
I view backup methods as 2 copies being necessary, a 3rd copy being ultimate but sometimes not worth the cost. I would use the control center of BackupExec to set up all of your systems to backup to a NAS overnight. Then, you can use either BackupExec or some other method to copy those backups to the MyBooks during the day. You could put backup data in the cloud, but that's a cost I don't think you need to incur unless you want a 3rd copy. If your business has multiple locations, your third copy could be located at one of these places, with its own NAS - essentially building your own online, offsite backup with technology you're already paying for.
Your NAS should have some sort of RAID... RAID 5 for redundancy and capacity. RAID 10 for redundancy and speed.
Do you want some assistance in picking out a NAS device? There are a lot of NAS threads already in the forums. You can build your own, buy a ready-made NAS, many options. Some of the ready-made NAS devices are easily integrated into Active Directory.