Autonomous aerial transportation has multiple potential applications including emergency cases and rescue missions where ground intervention may be difficult. In this context, the following work will address the control of multi-agent Vertical Take-off and Landing aircraft (VTOL) transportation system. We develop a decentralized method. The advantage of such a solution is that it can provide better maneuverability and lifting capabilities compared to existing systems. First, we consider a cooperative group of VTOLs transporting one payload. The main idea is that each agent perceive the interaction with other agents as a disturbance while assuming a negotiated motion model and imposing certain magnitude bounds on each agent. The theoretical model will be then validated using a numerical simulation illustrating the interesting features of the presented control method. Results show that under specified disturbances, the algorithm is able to guarantee the tracking with a minimal error. We describe a toolbox that has been developed for this purpose. Then, a system of multiple VTOLs lifting payloads will be studied. The algorithm assures that the VTOLs are coordinated with minimal communication. Additionally, a novel gripper design for ferrous objects is presented that enables the transportation of ferrous objects without a cable. Finally, we discuss potential connections to human in the loop transportation systems.