1. A network control system for configuring a logical network, the network control system comprising: a first controller instance, executing on a controller computer for receiving (i) configuration data for configuring a logical middlebox and (ii) logical network data that define a logical network topology comprising the logical middlebox and a set of logical forwarding elements; and a second controller instance executing on a host machine of a plurality of host machines managed by the network control system, the second controller instance for: receiving, from the first controller instance, (i) data records defining the logical middlebox configuration and (ii) forwarding data for the logical network; customizing the forwarding data for a managed forwarding element that executes on the host machine; and distributing (i) the customized forwarding data to the managed forwarding element for implementing the set of logical forwarding elements and (ii) the configuration data to a middlebox instance operating on the host machine for implementing the logical middlebox.