Successful application of evolutionary algorithms for large scale practical problems requires careful consideration of all the different elements of the applied evolutionary approach. Recently, a method was introduced for automatic matching of connections in a closed-loop control system that uses evolutionary algorithm in conjunction with model checking. In order to improve the method we consider using the permutation-based individual encoding, as it more realistically reflects real life scenarios, where the connections are matched on a one-to-one basis. Evaluation of the fitness function based on the model checking is computationally expensive, thus it is necessary to choose the best mutation operator in terms of the number of fitness function evaluations required to find the optimum solution. In this paper we evaluate the applicability of the permutation-based encoding for the problem of connection matching in the closed-loop control system and evaluate the performance of several permutation-based operators commonly used for ordering problems.