To simulate an operational amplifier in Simulink, a configuration using two adders and a gain block is recommended, with a high gain setting and a saturation block to limit output. Issues arise when trying to connect resistors and capacitors to the sum block due to incompatible signal types; the sum block requires pure numerical signals while resistors and capacitors use voltage signals. To resolve this, a Voltage Measurement Block and a Variable Voltage Source can be used to convert signal types appropriately. Additionally, a controlled voltage source is necessary to convert the output from the saturation block back to a voltage signal for measurement. Users are encouraged to explore block configuration panels for further understanding and troubleshooting.