Optimisation during the design of large manufacturing systems is a key issue. An adequate modelling formalism to express the intricate interleaving of competition and cooperation relationships is needed first. Moreover, robust and efficient optimisation techniques are necessary. This paper presents an integrated tool for the automated optimisation of DEDS, with application to manufacturing systems. After overviewing optimisation problems in Manufacturing Systems, it presents the integration of existing tools for the modelling and evaluation with Petri nets and a general-purpose optimisation package based on Simulated Annealing. Two application examples show the benefits of the proposed technique.