The entity controls the Empty and he explained to Castiel that the Empty existed before God or the Darkness.
When angels and demons die, they go to the Empty where they eternally slumber, allowing the entity to do the same.
Not even the combined power of God and the Archangels could destroy her, so God tricked and sealed her away by using the Mark of Cain as a lock and key.
God revealed that he chose not to kill her in her weakened state as she needed to exist with himself so reality wouldn't be destroyed.
It arose in the form of a pool of dark liquid inside the Empty after Castiel walked by before taking on a vague humanoid form.
The Entity followed Castiel as he made his way through the Empty, though he sensed the entity's presence and called out to it.
Possibly Pseudo-Omnipresent (Should be equal to God.