Drones have experienced rapid technological advancements, leading to the proliferation of small, low-cost, remotely controlled, and autonomous aerial vehicles with diverse applications, from package delivery to personal transportation. However, integrating these drones into the existing air traffic management (ATM) system poses significant challenges. The current ATM infrastructure, designed primarily for traditionally manned aircraft, requires enhanced capacity, workforce, and cost-effectiveness to coordinate the large number of drones expected to operate at low altitudes in complex urban environments. Therefore, this study aims to develop an intelligent, highly automated drone management system for integration into smart city transportation networks. The key objectives include the following: (i) developing a conceptual framework for an intelligent total transportation management system tailored for future smart cities, focusing on incorporating drone operations; (ii) designing an advanced air traffic management and flight control system capable of managing individual drones and drone swarms in complex urban environments; (iii) improving drone management methods by leveraging drone-following models and emerging technologies such as the Internet of Things (IoT) and the Internet of Drones (IoD); and (iv) investigating the landing processes and protocols for unmanned aerial vehicles (UAVs) to enable safe and efficient operations.