To optimize your HVAC system design using the Flexible Duct Calculator, start by inputting the required parameters, such as duct diameter, airflow, length, and number of bends. The calculator will provide the resulting friction loss, velocity, and equivalent rectangular duct size. Use these results to iterate on your design, adjusting parameters to achieve the desired airflow, pressure drop, and system performance. By repeatedly using the calculator and refining your design, you can optimize your HVAC system for maximum efficiency, reliability, and cost-effectiveness.