When built, quantum repeater networks will require classical network protocols to control the quantum operations. However, existing work on repeaters has focused on the quantum operations themselves, with less attention paid to the contents, semantics, ordering and reliability of the classical control messages. In this paper we define and describe our implementation of the classical control protocols. The state machines and packet sequences for the three protocol layers are presented, and operation confirmed by running the protocols over simulations of the physical network. We also show that proper management of the resources in a bottleneck link allows the aggregate throughput of two end-to-end flows to substantially exceed that of a single flow. Our layered architectural framework will support independent evolution of the separate protocol layers.