This work seeks to study one of the most complex and important issues in production scheduling research: flexible job shop systems. These systems are extremely important for industry, which uses the make-to-order strategy and seeks mix and volume flexibility. The model system will use agents within discrete-event simulation models, generating a Hybrid Simulation model. The agent will sequence the production orders at the beginning of the process and re-sequence them, when necessary, in order to achieve a multi-objective optimization. For this, the agent will bring together two different logics that have opposing goals. This work consists of the comparison of the results of three scheduling methods: firstly, with the sequence of arrival; secondly, with the agent using one sequencing logic; and, finally, using the same logic, but with adjustments in the sequence during the batch production, seeking to improve the negative points generated by the logic. It also stresses that this schedule ensures that the Manager Agent reduces makespan and increases machine utilization while increasing its interference in the model. This is a quantitative study, using the modeling and simulation method and following an empirical model.