How do they prepare a damaged skull for a closed casket funeral?

You answered your own question, if the casket is closed- there is no viewing, so no need to cosmeticize the remains, apart from health considerations- he or she would be embalmed, and one hopes, dressed. as the legal phrase goes- this case is closed. a photograph of the deceased- say good portrait head-shot ( no pun intended) should be prominently displayed to show what the deceased looked like in life!