Sorry for the slow response, here are the answers to your questions.
1)
Please have a look at the help documentation for the “Er Doped Fiber”. It actually does quite a good job at explaining the calculation of the gain.
2)
The bandwidth of the filter is a parameter you set. It depends on the signals bandwidth. For example for the DSP the best bandwidth of the electrical Bessel filter is 0.75*Symbol rate. For the optical filter we generally choose it to be larger than the signals bandwidth. In WDM applications you should make the bandwidth large enough to get all the signal but not too large to overlap the other channels.
3)
Please look in “OptiSystem12 Samples / Advanced Modulation Systems / RZ (50RZ, 33RZ, 67CSRZ, Chirped, Alternate-Chirp, VSB)”. We show a number of designs.