I have managed to do a clean install of OS X El Capitan on a Mac with a Fusion Drive.
1. Download the OS X El Capitan App from the Mac App Store.
2. Using an empty 8GB or larger thumb drive, plug in the thumb drive into an unused USB drive on your Mac.
3. Open up Terminal by pressing cmd + space bar on your keyboard and type Terminal and hit return on your keyboard.
4. At this step, make sure that you don't have anything important on the thumb drive as the next step will reformat it. Also, make note of the name of your thumb drive by looking at your thumb drive on your Desktop. In my example, I will use the name UNTITLED for my thumb drive.
5. In Terminal, type the following command, all one line:
sudo "/Applications/Install OS X El Capitan.app/Contents/Resources/createinstallmedia" --volume "/Volumes/UNTITLED" -- applicationpath "/Applications/Install OS X El Capitan.app"
6. You will be prompted to enter your password.
1. Now that you have your OS X El Capitan install media, you will need to reboot your into the Recovery partition and NOT your OS X El Capitan thumb drive. To boot into your Recovery partition, reboot your Mac and hold down the cmd + R key on the keyboard. Keep holding cmd + R until you see the Apple logo.
2. You will see the OS X Utilities window, in there, click on Disk Utility.
3. On the left side of the Disk Utility window, click on Macintosh HD, and click on Erase, and then on Erase again to begin the process.
1. Now, if you, like me, made the mistake of directly booting into the OS X El Capitan thumb drive, and tried to use the Disk Utility from El Capitan to erase your Macintosh HD, you will notice that it will error out. So perhaps you decided to boot back to the Recovery Drive and tried to erase the disk again and still nothing. Well you can use the Terminal, to bring back your Macintosh HD. (Note: I performed the following steps in the Recovery partition using the Terminal there. I do not know if this will work in the Terminal in the OS X El Capitan thumb drive media. But the commands are identical to try and erase the Macintosh HD and bring it back up.)
2. Launch Terminal by clicking on Utilities and then click on Terminal.
3. In Terminal type the following command to list your disks:
diskutil coreStorage list
4. From here look for the UUID for Logical Volume Family. The UUID is a universally unique identifier that is randomly generated when the Fusion Drive is created. This is the combination of the solid state drive and the hard disk drive on your Mac. The Logical Family Volume is the representation of these two physical drives combined as one logical disk known as the Fusion Drive. From this logical disk, your Fusion Drive, we will need to create a logical volume to which you will install OS X El Capitan. To do that, in Terminal, type the following command to re-create your Macintosh HD using the UUID for the Logical Volume Family. In the example below, I will use de305d54-75b4-431b-adb2-eb6b9e546014 as my UUID, this will be different from yours:
diskutil coreStorate createVolume de305d54-75b4-431b-adb2-eb6b9e546014 jhfs+ "Macintosh HD" 100%
4. Now wait for this to complete. Once done, if you are in the Recovery partition, reboot your Mac and hold down the option key on your keyboard and wait for the screen to show the drives, and simply click on your OS X El Capitan thumb drive and install OS X El Capitan on a clean Fusion Drive.