I have the type of data storage setup you describe. Firstly, I have partitioned the 1TB Fusion drive into the maximum allowable two partitions:
1) Macintosh HD (all the system files) - this bit lives entirely on the SSD part of the Fusion drive for performance.....
2) ..... and Media which I use for iTunes and video storage. Because this type of data doesn't benefit from SSD speed, the partition scheme forces the Media partition to live solely on the spinning part of the Fusion drive.
I have added an external Thunderbolt 1TB LaCie SSD Little Big Disk (RAID1 stripe).....
3) .... to create a Users volume. I have relocated all of the iMac's four user's home directories onto this external drive. In particular, my 200gig Aperture library lives here.
I bought into the concept of strict separation between system and user data hence relocating user home folders away from the system volume. Use of LaCie allows me to put all user data on very fast SSD at a cheaper price point than the internal Apple SSD option (even after the price drop). And partitioning the Fusion drive allows me to force media that doesn't benefit from SSD onto the spinning part of the drive.
For backup, I have two portable USB3 drives - a 1TB and a 2TB, both WD My Passport. They are attached behind the 27" monitor to the main support via elastic bands. The smaller one is partitioned into three disks (Boot, Media and Users) and I use Carbon Copy Cloner to clone each of the three logical disks mentioned above on a weekly basis. The larger one stores Time Machine backups of all three.
If I have a problem with the Fusion drive in the future, I can boot from the 1TB "Boot" partition. All the other disks are cloned for fast restores. All user data can be unplugged from the iMac if it needs to go back for repairs. If I need granular restore, I can use TimeMachine.
The really cool feature of this generation of iMac is the very fast Thunderbolt interface (so I can locate primary user data storage externally) and USB3 for fast backup. The system now takes on many of the characteristics of a Mac Pro from the standpoint of data storage. Make sense?
Nikko