To plot transmission as a function of wavelength you need to simulate the identical experimental setup. To be more clear, how you are going to couple light in and out of devices and whether injected light is TE or TM polarized. This would directly effect the modes that you can excite and also the coupling coefficient (depth of each resonance). As an example, you can use a waveguide that evanescently couples light into devices.
For bandstructure calculations we use dipole source at different locations and orientations to make sure that we are exciting all the modes. This is a general approach to make sure that we have a full knowledge of all the PC modes. However in a real experimental setup we might not be able to capture all the modes.
Generally speaking, you expect to see a dip on transmission plot at the resonance frequencies. The bandwidth of this dip depends on the optical quality factor and depth is controlled by coupling coefficients.There are plenty of examples how people measure the PC cavities that you might find them useful to begin with.
Similar scenario holds if you have a PC waveguide. Basically, you expect to see no tranmission on the bandgap.