I have the following setup to backup my iMac and rMBP using a combination of Carbon Copy Cloner (CCC), Time Machine, and CrashPlan. May sound like overkill, but I feel pretty safe with it.
Drives needing backup:
-iMac 628GB "fusion" drive
-rMBP 256GB SSD
-External Media Drive 2TB
External Disk 1 Backup - 1TB
-Partition 1 - 700GB -Time Machine Backup for iMac
-Partition 2 - 300GB -CCC Backup for rMBP (bootable clone)
External Disk 2 Backup - 1TB
-Partition 2 - 300GB -Time Machine Backup for rMBP
-Partition 2 - 700GB -CCC Backup for iMac (bootable clone)
CrashPlan (unlimited space) backs up:
-iMac 628GB
-rMBP 256GB
-External Disk1 1TB
-External Disk2 1TB
-External Disk3 2TB (with movies/tv shows only)
Alternatively, the External Disk3 is also manually replicated about once a month to an external drive at my parent's house (so my kids can watch movies when with them via ATV). Their computer has the same backup scheme above (minus the rMBP), so technically my external disk 3 (movies) are backed up to their CrashPlan account as well.
So in hardware/investment for backups I have 2x 1TB drives for backup ($79/ea), and a CrashPlan account ($60/yr - look for deals around end of November)....and another $129 if you want to add in the disk3 backup at my parent's house.
With all of this I've used TM and the bootable clones both as restores and never had an issue. And I never used the WD software, but still have also not moved my iMac to Mavericks yet...need to do some more research on its affects on the homemade "fusion" drives...