This paper presents the software-defined management system of DC-QNet, a quantum network testbed deployed across multiple distant sites. The system uses a network management system (NMS) to manage the optical network, the classical IP network, and the quantum equipment involved in a quantum networking experiment. The NMS also implements a measurement plane that abstracts the heterogeneity of equipment and measurement complexity. The management system provide the ability to establish optical channels between quantum devices, control the devices, and support an extensible measurement plane that enables the automated setup and execution of experiments. The testbed and its management aim to simplify experiments and improve the efficient management of resources in the development of functional quantum networks.