The simulator window is the graphic manifestation of the simulation engine. The simulation engine has the job of keeping track of river basin components (confluences, diversions, reaches, reservoirs and tables), their relationships and their data sources. What is shown in the window is a faithful mirror of the underlying model's structure. Changes to the graphic structures are instantly reflected in the model. Thus, when you change the linkage between two nodes, that changed state is the one with which the model will execute. It is NOT the case that your graphic changes are translated to some file which is then used as input to a modeling code.

Each of the icons and links in the simulation window is an object which maintains an internal state and which manifests specified behavior. The simulation engine executes the meta algorithm.