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The widespread of overlay networks are explaining by the benefits of supporting customized control and forwarding functions over an existing network. However, overlay networks increase the complexity of managing the configuration of the supporting (physical) network. This paper proposes a management architecture for configuring the physical and overlay (logical) networks in an integrated way. The components of the architecture and their relationships are presented, as well as an implementation of the architecture, the Onix system. Onix allows the configuration of both physical and logical networks and employs several design patterns in its conception.