Witch Bottles originally were used as a counter-ritual to witchcraft or evil spells. It was supposed to keep the evil witches away and work against their spells and was often tucked away in the walls or foundation of a house.
Now, they are used by Wiccans and Witches as spells to keep evil away. (Most Wiccans and Witches are involved in White Light and not evil/darkness.) Except instead of filling them with urine and teeth (and other yucky stuff) things like herbs, crystals and other positive items are in them. You can bury them, hang them, or simply sit them on a shelf.
As with all things of magic, it's the intention that manifests the "magic". If intentions are good, that is what will manifest.