The objective of this research is the study of container terminals with two separated piers within the same port basin. The main problem is how to optimize the berth and crane allocation and to minimize the overall service time for the vessels and to improve the utilization of the terminal assets. The optimization of the seaside subsystem of the container terminals combines three typical operational problems: ship-to-berth allocation, quay-crane to ship assignment and quay-crane scheduling. Due to their characteristics, they have a high correlation and should be considered together. The problem can become even more complex in the Container terminals with a different layout where quays and berths are not placed in the line or where berths are situated in different piers. In this paper, a specific methodology is presented with a focus on the optimization process. This process consists of three stages namely: initiation, allocation and adjustment. The core of the problem solutions in stage 1 is the execution of crane scheduling problem according to cargo volume and container distribution on the vessel. The result of this stage is three operational scenarios that set out two key variables: duration of the handling process and the number of cranes required. According to the results from stage 1, ship-to-berth assignment and allocation of cranes isexecuted. The practical approach implemented here, targets to high prediction, reliability and efficiency of the operational plans to satisfy the requirements of the shipping companies. This approach requires a fixed number of quay- cranes during the handling operations and high utilization rate of the cranes. The results of the overall optimization have been shown on the few examples