If my inputs stay the same but my crop yield increases, will my Energy Use and GHG emissions decrease?

Yes, intensity-based metrics (metrics based on crop production output, like per bushel) look better with higher yield values. However, it is important to evaluate both dimensions: look at indicators expressed per area (e.g., lb CO2e / acre) as well as per production output (e.g., lb CO2e / lb of crop output). Reviewing both ensures you do not mask an increased use of inputs that might have been required to achieve those higher yields.