1. A method of processing a logical netlist for implementing a circuit design within a programmable integrated circuit, the method comprising: identifying a dynamically reconfigurable module (DRM), comprising a port, from the logical netlist, wherein the DRM defines a dynamically reconfigurable region of the programmable integrated circuit that communicates with a module of the logical netlist that is not dynamically reconfigurable via the port; determining, by a computer system, whether the port connects with circuitry within the DRM as specified by the logical netlist; when the port connects with circuitry within the DRM, selecting connection circuitry connecting the circuitry within the DRM with circuitry that is external to the DRM within the module that is not dynamically reconfigurable; when the port does not connect with circuitry within the DRM, selecting connection circuitry of a particular type connecting the port of the DRM with circuitry that is external to the DRM within the module that is not dynamically reconfigurable according to an attribute associated with the port; and updating, by the computer system, the logical netlist to specify the connection circuitry.