Being high in relation to destination airport, the flight instructor of the multi-engine airplane initiated a steep descent with the throttles at idle. During the descent, the landing gear warning horn sounded, which the flight instructor thought was the stall warning. After descending to traffic pattern altitude, the flight instructor transferred control back to the multi-engine student, who joined base-to-final leg of the airport traffic pattern. The student subsequently recommended either performing a go-around or squaring the base turn to final approach for landing. The flight instructor directed him to perform “S-turns” which he felt uncomfortable doing and the tower controller instructed them to maneuver as needed. The student then transferred control of the airplane back to the flight instructor either on the base leg or short final approach. While on short final approach (likely due to cockpit annunciation of either the radio altimeter or throttles being at idle with the landing gear not extended) the flight instructor recognized that the landing gear was not configured for landing and initiated a go-around. The airplane was too low and subsequently contacted the runway with the landing gear retracted, resulting in substantial damage to the underside of the fuselage. After raising the airplane from the runway, the landing gear was extended using the normal system with no reported issues.