People with reduced mobility often face challenges when using current regular public transportation systems. However, there is an observed increase in door-to-door services. The implementation of an alternative system targeted to a specific and non-scaling audience, requires greater flexibility while simultaneous being able to minimize service costs, introducing new challenges and uncertainties during its implementation. Some systems fail due to strategic errors made during planning, related to configurations and the choice of less appropriate resources. This underscores the need to design a framework capable of capturing the heterogeneity and interactions of interests simultaneously, involving stakeholders in the decision-making process by providing essential information and perspectives. This article explores the methodology employed to create an intelligent management framework for a flexible transport system, consisting of three main components: operational management, simulation, and decision support system. The interconnection of these elements will enable an understanding of the context, resource optimization, adaptation of parameterisation to existing needs, solution evaluation, comparison of alternative scenarios based on different criteria, real-time system monitoring/control, and assessment/investigation of incidents, non-conformities, and risks. This way, valuable information will be provided to define structure of resources and technologies that best address the real needs of the field, ensuring that solutions reflect the preferences of stakeholders.