Q: How do you format a Fusion drive in El Capitan - won't combine SSD and non-SSD into Fusion drive like it did in prior OS versions

I have a DIY Fusion Drive in my Mac Pro. It is working fine since I have upgraded to El Capitan.

The directions I used to create it are from http://blog.macsales.com/15617-creating-your-own-fusion-drive

I ran into the same problem when I tried to  "clean install" El Capitan on my 2012 27" iMac with factory fusion drive.  I booted into internet recovery and used the disk utility there to "fix" the fusion drive.  I then was able to restart and select my usb installer to install El Capitan.  If you do not have a bootable installer for El Capitan you would have to install the original OS that your iMac came with.  The disk utility for Lion thru Yosemite will fix your fusion drive; disk utility in El Capitan (version 15) will not, however with El Capitan you don't have to do the coreStorage delete to clean install.

Simply erase the Macintosh HD and it will erase but leave your drives fused.

P.S use migration assistant to re install your apps settings and data.  Choosing restore from a time machine back up might cause problems.

Use the info near the end of this post vel capitan update wiped my details

Best of Luck: Tom