I just upgraded El Capitan on my Asus P9X79 pro computer.
Before, I was using Yosemite. Like you !
To be able to boot from your usb key, you need to set
GraphicsEnabler=No npci=0x2000 and nv_disable=1
You can also add -v.It is faster without.
Under Clover selection screen :
- type "O" then use down key to options box,
- hit space to edit it,
- return key when done,
- Return at the bottom of the list ->
- choose your UsbKey ... and boot !
If you plug your usb key on the front panel of your computer, you will get a
"Still waiting for root device"
error code (if -v was enabled, otherwise, you will not be able to read this error).
Simply plug your Usb key, on a free usb2 slot on your motherboard and boot will succeed ! You will be able to install El Capitan
Reboot with your usb key and follow the procedure from Tonymac !
Edit : I have not disconnected anything, and I simply used default bios settings to install El Capitan