The problem of resource allocation and scheduling is considered for a flexible job shop composed of several work centers with multiple identical machines. Each machine has its own setup time that depends on the current and the arriving batch types. The optimal number of machines at each center and the optimal batch size for each job type is to be determined for several dispatching rule. The objective of the study is to assist the scheduler in selecting the best dispatching rule with respect to a desired performance measure along with its corresponding batch size and optimum number of machines in each center. Several measures are considered including the average flow time, sum of earliness and tardiness, and the number of tardy jobs. The simulation package ProModel is used to build the model and its optimization tool called SimRunner is used for optimization.