Changing substrate concentration will reduce the rate of the enzyme it is the substrate for, as described by Michaelis-Mentin kinetics. However, this will likely not have an impact on the rate of the entire pathway, as it is likely that another enzyme will be rate limiting.
Metabolic flux analysis allows the study of how energy flows through metabolic pathways, and can be used to identify rate limiting enzymes. If the rate or concentration of the limiting enzyme is increased, it is unlikely to make a large difference to the overall flux of the entire pathway. This is because another enzyme will become rate limiting and restrict the flux of the overall pathway.
The impact of substrate concentration can also be studied by metabolic flux analysis, identifying how the pathway changes in response to different concentrations of substrate.