Hi Stavros,
It might be slightly different in OptiFDTD 8, but you can look at the tutorial on band gap simulations at:
To perform a transmission vs wavelength type simulation, try a Gaussian Modulated Continuous Wave pulse as your input field. A very short pulse will have a large amount of frequency content. Then at the output place an Observation Area. Once the simulation is done, you can view the normalized (w.r.t Input Plane) Power detected as a function of wavelength. Again there is a tutorial that might make it clearer for you.
Hope this helps!