If a darkskull was embeded into a clockwork creature, what would happen? Would the unhallow spell continue while the clockwork creature moves? Would it be a moving unhallow spell and all the affects of the spell continue in that area? Also since it is an artifact, can it be destroyed by any conventional means?
Darkskulls are not artifacts. They are just another magic item.
And the area of the unhallow effect (and its attached spell) would move with the clockwork creature, just as it would move when being carried by someone.
It's not an artifact, it has both a market price and a creation cost, and can be built using the feat Craft Wonderous Item. There is even a non-evil variant:
The Ruby Skull of Chast
And as I understand it, the Unhallow effect / spell / area would move with it.