Petri nets are well suited for modelling production systems and analysis of their performance. In this paper we study a flowshop system driven by a set of local command units and a central controller, modelled with Timed Coloured Petri nets by means of CPN Tools. We show that Petri nets can be applied not only to improve its production rate by comparing various algorithms for the controller policy service, but also to analyse the significance of parameters as conveying and mechanical delays, maximum work-in-process or to understand problems appeared in the real system