To restore Balance to the Serpent Isle, you will need to perform a couple of rituals to restore and realign the Serpents of Order, Chaos, and Balance. They're all pretty straightforward.

To restore the Chaos Serpent:
You must have the Banes trapped in the Soul Prisms. Follow the Chaos Hierophant's instructions, he should have given you a scroll detailing the ritual. Lay the blackrock chaos serpent in the slot on the floor. Put each Bane on the altar corresponding to it's Force. Single click on the prisms to see which Prism is holding which Bane. Insanity goes with Emotion. Wantoness goes with Enthusiasm. Anarchy goes on Tolerance.

To restore the Great Earth Serpent:
Place all three blackrock serpents in their slots. Place the Chaos and Order Serpent eyes on the altar, and then kill the blackrock serpent statue with the Ophidian sword.