A network control system for generating physical control plane data for managing first and second managed forwarding elements that implement forwarding operations associated with a first logical datapath set is described. The system includes a first controller instance for converting logical control plane data for the first logical datapath set to universal physical control plane (UPCP) data. The system further includes a second controller instance for converting UPCP data to customized physical control plane (CPCP) data for the first managed forwarding element but not the second managed forwarding element.