Frequent changes in customer needs and large product variety are forcing manufacturing companies to move from mass production to mass customization. Customized production can be achieved by introducing reconfigurable production systems (RMS). The customized flexibility and several characteristics of RMSs provide many opportunities in terms of process and production planning. However, those characteristics greatly increase the complexity of the design and planning of production systems. This paper presents a decision support system relying on a skill-based approach to design a reconfigurable assembly line considering the planning of assembly processes and monitoring. The proposed decision aid system is modular in design and is composed of four modules. The main input data is a CAD model of a new product variant for the identification of the assembly and monitoring requirements. Besides, a current assembly system layout with its resource descriptions exists. In the first developed module, assembly-by-disassembly and a skill-based approach are used to generate different assembly plans. In the second module, feature recognition and skill-based approaches generate process monitoring alternatives. The third module uses a linear program (LP) that aims to minimize the total cost of workstation activation and reconfiguration, as well as cycle time, and to maximize the process quality of the assembly tasks. A user-based generative model design approach is applied to optimize the values of three objective functions. In the fourth and final module, a simulation of the optimized assembly plan allows either the validation of the assembly plan and process monitoring plan or initiates a new iteration due to their infeasibility. To further demonstrate how the proposed methodology works, some computational experiments are provided for two use cases.