The paradigm of the cyber-physical manufacturing system is playing an increasingly important role in the development of production systems and management of manufacturing processes. This paper presents an optimization model for solving an integrated problem of production planning and manufacturing control. The goal is to create detailed production plans for a complex manufacturing system and to control the skilled manual workers. The detailed optimization model of the problem and the developed approach and algorithms are described in detail. To consider the impact of human workers performing the manufacturing primary operations, we elaborated an extended simulation-based procedure and new multi-criteria control algorithms that can manage varying availability constraints of parallel workstations, worker-dependent processing times, different product types and process plans. The effectiveness of the proposed algorithms is demonstrated by numerical results based on a case study.