It would be a good idea if you first make a bootable backup of everything on the Raid Mac Mini to an external drive. You can use either SuperDuper! (
http://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html) or Carbon Copy Cloner (
https://bombich.com/). Either of them are excellent at making exact an exact copy/clone of what you want to backup. And, each such backup is bootable. The primary difference between them is that Carbon Copy Cloner will also back up the (hidden) Recovery Partition. Both of them are available in "demo" mode for 30 days, and for the "basic" copying/cloning, they work just like the paid versions.
I assume you have already downloaded the OS 10.11.2 full installer from the App Store. (You should also make a copy of that file in another location). Also, I assume you have insured that whatever third party software you are running is either already compatible with OS 10.11.2, or else has been upgraded,
Now, once you do that, you can proceed in one of two ways. One of them is to re-boot from the external drive/partition containing the bootable backup (that of course will be Yosemite). You could then run Disk Utility from that backup to Erase and Format (and if necessary, Partition) the "Raid" array on the Mac mini. Then, you would launch the file "Install OS X El Capitan" located on the Applications folder, and do a clean installation of OS 10.11.2 onto the location on the Mac MIni that you choose. (That "Install OS X El Capitan" will disappear after you are done, so that is why I mentioned above about making a copy of it somewhere else). Finally, re-boot from the Mac Min i, and use Migration Assistant to "migrate"/copy all the non-system stuff from the backup to the Mac Mini.
The other choice is to launch the file "InstallOS X El Capitan" file while you are booted from the Mac Mini, and do an upgrade from Yosemite to El Capitan from there.
IN either case, if you encounter any issues, you can easily restore your system to the way it was at the start from the backup/clone made by either SuperDuper! or Carbon Copy Cloner.