Ok, I've just done a DIY upgrade and literally replaced all my drives by tripling the overall storage (everything replaced except the original Mac Mini 256Gb SSD) - the fun was documented in this thread here: http://talk.appletalk.com.au/t/diy-upgrades/2544/4
As such, my storage and backup strategy has been modified as per following:
The Mac Mini now has 2 x 256Gb SSDs. Originally, I was going to use 1 as the boot startup disk, and the other as a clone backup boot drive. But I decided to try to squeeze as much speed out the system as possible, and stripe both drives together as a 500Gb RAID0 striped partition, and use that as the main boot drive.
Interestingly, in El Capitan, I couldn't find the RAID tab in Disk Utility anymore - Apple had removed it! You can now only set up software RAID in OSX via terminal using the following command:
diskutil appleRAID create stripe NameOfDrive JHFS+ disk0 disk1
(obviously use the correct disk device id).
Anyway, the Mac Mini boots off the 500Gb SSD in RAID0, which makes it quite fast now, and I keep my OS and apps on it.
Data is still kept on the Thunderbolt Promise Pegasus R4, but it now has 4 x 3Tb 7200rpm HDDs in it - 12Tb total - initially I was going to run it in RAID5, which would give me 9Tb, but I decided to opt for both speed and redundancy, so it is now in RAID10 giving me 6Tb of storage space, which is more than enough for me in the short to medium term.
I put the new 6Tb 7200rpm HDD in the Thunderbolt LaCie, which now serves as the local backup drive. I partitioned it into a 250Gb partition, which now serves as the Carbon Copy Cloner cloned boot disk, which I used initially to boot up in, to set up the RAID0 for the internal SSDs. At the moment, I will clone the boot drive once a week.
The other 5.75Tb partition now serves as my local Crashplan folder backup for the data off the R4 (before I was using rsync running off a Calendar event through an automator script in app, but Crashplan allows for versioning and roll-backs, like Time Machine but better).
The R4 data also backs up to the Crashplan+ cloud as well, so I have both local and off-site backup of my data.
As before, my work documents syncs to Dropbox Pro, replicated across my laptops.
So there you go, my new setup.