The parameters that are configured in NetSim GUI are written to a Configuration.netsim file when you run the simulation. You will find this file in folder %temp%/NetSim (Go to start -> run -> Type %temp%/NetSim) or in the Experiment folder present in the workspace after saving the scenario.
Reading the parameters to initialize simulation parameters for the protocol stack is taken care of by NetSim's simulation engine internally.
Each parameter that is read is stored in a respective variable that can be accessed during runtime. This generally happens in the fn_NetSim_<protocol>_Configure() function which is part of the main C file in every Visual Studio Project (Eg. TCP.c, IEEE802_15_4.c, DSR.c, etc).
For instance, if we look at 802.22 cognitive radio networks, the variables related to the Physical layer parameters of the Secondary Users (CRCPE's) are declared in the 802_22.h file under struct stru_802_22_CPE_PHY where dTXPower is used to store the transmit power of the Secondary user. To obtain the transmit power configured for any of the secondary user in the code, DEVICE_PHYVAR(DeviceID, InterfaceID)->dTXPower can be used.
Where,
DeviceID is the unique ID of a CRCPE
InterfaceID is the unique ID of the interface in which it is connected to the BS.