A custom prototyping board and a controller are integrated to form an emulation system for emulating a circuit design. The controller may be disposed on an adaptor board. The custom prototyping board is defined by a set of board description files which further define the FPGA device(s) used in the system as well as the wire connections among the FPGA devices and connectors on the custom prototyping board. The FPGA device(s) is configured in accordance with the partitioned circuit design. Each partitioned circuit in the FPGA device is associated with a verification module for communicating with the controller to control and probe the emulation. A host workstation may be used to link with the controller to support co-simulation or co-emulation of the circuit design.