To subtract photocurrents from two photodiodes using a lock-in amplifier, the SR830 model can be utilized effectively. First, measure the currents from both photodiodes with the lock-in amplifier by connecting the reference frequency to the reference input and the signals to the measurement input. After obtaining the current measurements, the outputs can be fed into a storage oscilloscope for subtraction to analyze the difference in photocurrents. Understanding the settings for sensitivity, reserve, and time constant on the lock-in amplifier is crucial for accurate measurements. Consulting the lock-in amplifier's manual is recommended for detailed operational guidance.