There are two main theories as to the reason for depositing the horse skulls in buildings: as a method for enhancing the acoustics of a room, such as in a church or in a threshing barn; or as a method for repelling evil spirits such as witches and ghosts.[1]
Manning, M. Chris (2012), Homemade Magic: Concealed Deposits in Architectural Contexts in the Eastern United States Master's thesis, Anthropology Program, Ball State University, Muncie, IN.