Many manufacturing systems must operate under resource constraints. Simulation can help to improve the operation of such manufacturing systems. This paper presents a practical approach how to conduct a simulation project. A Flexible Manufacturing System (FMS) was chosen for the simulation. The targets for FMS improvement were given. A set of measures was proposed to meet the given targets. Design of Experiments (DoE) was used to minimise the number of simulation experiments. There were simulated and evaluated various measures and control strategies and their influence on the FMS characteristics. Rough cost analysis of each simulated variant was done. Futurę research targets are presented.