A configuration manager identifies a first device and a second device within a simulated system. Each device within the simulated system includes an inbound port and an outbound port. Next, the configuration manager injects a simulation only packet on the first device's outbound port and detects that the second device's inbound port receives the simulation only packet. As a result, the configuration manager determines that a direct connection exists between the first device's outbound port and the second device's inbound port. In turn, the configuration manager configures one or more first device configuration registers and one or more second device configuration registers that correspond to the first device and the second device, respectively.