During crane operation, the task of retrieval and deployment of payloads can be partitioned into two components: the initial move towards the target or deployment location and the retrieval or deployment of the payload. If the payload is not stationary, as is the case in the retrieval of a sea-going vessel, a third component, tracking, must be included. The target payload in this research is an Autonomous Surface Vehicle (ASV) primarily used for surveying. This paper studies the transition between the initial move towards the payload and the initialization of tracking. Input Shaping is used to limit residual vibration caused by the initial move to the ASV. A set of Fuzzy Logic membership functions are then used to transition from the initial move to the tracking portion of the retrieval process. These membership functions map position and velocity error to a gain that is applied to the tracking controller. As the gain increases, the contribution of the tracking controller input is increased. Zero Phase Error Tracking Control is utilized for accurate tracking of the target payload. Through a combination of these control methods, the tracking accuracy is improved.