Ender essence can be created in the essence refiner by putting in 2 eyes of ender, 2 ender pearls and 1 arcane ash in the following configuration below. It is used for spell recipes with the damage modifier,which can increase the damage of your spell.
(Note: For this to work, you need to have used a Crystal wrench and link an Obelisk with power by putting an Etherium bucket in it to provide power for the refiner to work. )