I used it in the whole loop. And I have the same. Ek supremacy, and xspc AX360 rads with ek pump res combo.
From how I read the instructions, that's how I understood it.
Take your time filling it up. It foams a lot! As your doing so make sure you vent any trapped air.
The foam settles down inside the loop after half hour or so, after an hour tilting the pc around whilst the pump is running gets most of the air out of the system.