So as you might be aware many of the components add noise to the signal through noise bins, EDFAs for example. The PIN adds noise directly to the sampled signal and not as noise bins. However the Electrical Amplifier does add noise as a separate signal. On the Noise tab of these amplifiers there is an option to add noise to signal, if you check the box the separate noise signal will disappear and the total noise will be added to the sampled signal.
Also just use the BER Test Set, instead of the BER Analyzer it can be found in the Test Sets folder.