Collaborative industrial systems are becoming an emergent paradigm towards flexibility. One promising solution are service-oriented industrial automation systems, but integrated software methodologies and major frameworks for the engineering are still missing. This paper presents an overview of the current results on a unified and integrated methodology based on intrinsic and novel features of Petri nets. These nets are applied to the modeling, analysis, service management, embedded software controllers, decision support system and monitoring, to improve the fundamentals in the engineering of service-oriented automation systems. The solution may contribute to the reduction of the design, operational and reconfiguration phases in the life-cycle of novel automation environments. Results were obtained and discussed from simulations and real industrial demonstrators.