We introduce a new model and mathematical formulation for planning crane moves in the storage yard of container terminals. Our objective is to develop a tool that captures customer centric elements, especially service time, and helps operators to manage costly relocation moves. Our model incorporates several practical details and provides port operators with expanded capabilities including planning repositioning moves in off-peak hours, controlling wait times of each customer as well as total service time, optimizing the number of relocations and wait time jointly, and optimizing simultaneously the container stacking and retrieval process. We also study a class of flexible service policies which allow for out-of-order retrieval. We show that under such flexible policies, we can decrease the number of relocations and retrieval delays without creating inequities.