One of the major planning issues in large scale automated transportation systems is so-called empty vehicle management, the timely supply of vehicles to terminals in order to reduce cargo waiting times. Motivated by a Dutch pilot project on an underground cargo transportation system using Automated Guided Vehicles (AGVs), we developed several rules and algorithms for empty vehicle management, varying from trivial First-Come, First-Served (FCFS) via look-ahead rules to integral planning. For our application, we focus on attaining customer service levels in the presence of varying order priorities, taking into account resource capacities and the relation to other planning decisions, such as terminal management. We show how the various rules are embedded in a framework for logistics control of automated transportation networks. Using simulation, the planning options are evaluated on their performance in terms of customer service levels, AGV requirements and empty travel distances. Based on our experiments, we conclude that look-ahead rules have significant advantages above FCFS. A more advanced so-called serial scheduling method outperforms the look-ahead rules if the peak demand quickly moves amongst routes in the system.