In any case where the deed conveying lands and premises to the State of New York, for the uses and purposes of the reservoir, reserves a right of access or use, in respect to said lands and premises, such right of access or use shall be exercised in pursuance of the provisions of the deed relating thereto; subject, however, to these rules and regulations. Any person claiming to have any such right of access or use shall, before exercising the same, make and file with the board an application for a permit therefor and for renewal or renewals thereof, in accordance with these rules and regulations. All permits and any renewal or renewals thereof granted and issued in respect to any such right of access or use shall be so granted and issued in accordance with these rules and regulations. In any case where it is claimed that the deed reserves several rights of access or several uses or purposes in relation to lands and premises acquired by the State for the purposes of the reservoir, a separate application shall be filed for each such right, use or purpose, and the application and permit shall definitely and specifically set forth such right, use or purpose.