Cost of Permits. Permit fees are based on deck square footage and whether or not a zoning permit is also required. Decks less than one thousand square feet shall have a base fee of $100 (one hundred), while decks one thousand square feet or above will be priced depending on exact square footage.A $165 (one-hundred-sixty-five dollar) fee is added to the base fee for all residential decks requiring a county zoning permit.ecks less than one thousand square feet shall have a base fee of $100 (one hundred), while decks one thousand square feet or above will be priced depending on exact square footage. A $165 (one-hundred-sixty-five dollar) fee is added to the base fee for all residential decks requiring a county zoning permit.