This paper proposes the application of computer simulation methods in order to analyse the availability of resources, buffers and the impact of the allocation of workers on the throughput and work-in-progress of a manufacturing system. The simulation model of the production system is based on an existing example of a manufacturing company in the automotive industry. The manufacturing system includes both machining and assembly operations. Simulation experiments were conducted vis-à-vis the availability of the different manufacturing resources, the various allocations of buffer capacities and the number of employees. The production system consists of three manufacturing cells – each cell including two CNC machines – and two assembly stations. The parts produced by the manufacturing cells are stored in buffers and transferred to the assembly stations. Workers are allocated to the manufacturing cells and assembly stations, but the number of workers may be less than number of workplaces and are thus termed ‘multi-workstations’. Using computer simulation methods, the impact of the availability of resources, the number of employees and of the allocation of buffer capacity on the throughput and work-in-progress of the manufacturing system is analysed. The results of the research are used to improve the effectiveness of manufacturing systems using a decision support system and the proper control of resources. Literature analysis shows that the study of the impact of buffer capacities, availability of resources and the number of employees on assembly manufacturing system performance have not been carried out so far.