To setup the simulation to obtain the transmission spectrum simply setup an input plane across the waveguide, setup a Gaussian distribution centered at the waveguide with roughly the correct width. The source should be a pulse to give you broadband response. Then you setup an observation point or observation line (I am assuming you are still working in 2D) and when the simulation is done look at the data from the observer in the frequency spectrum.
Keep in mind you will need to tell OptiFDTD Analyzer that you want the results from the observer normalized to the source.
Scott