We calculated the transmission properties of the defect structure as we would have done for a slab of material or just another defect-free photonic crystal. The thing is, our work is mostly experimental. When doing the simulations we try to mimic the experimental configuration as much as possible. The reason for this is the following: if we do not follow such a methodology, our simulations may result in some really fancy conclusions, which do not reflect the real life. Anyway, As you mentioned, you may also calculate the defect modes by using fullwave. There is a very nice paper by K. Sakoda which explains the principles of such calculations. What does fullwave do to calculate the defect mode? A defect mode is a localized eigen mode. Hence if you place a point source at the center of the defect cell and excite the point source with and impulse function, you will observe some peaks in the fourier spectra of the signal recieved by a time monitor replaced at some point in the defect cell. Though there is no guarantee that such a peak will correspond to the actual defect mode. At least one of such peaks will correspond to the defect mode. In order to check wether such a frequency corresponds to the "actual defect mode", you need to calculate the steady-state field distribution due to a source placed in the defect cell. The frequency of the source must be set to the frequency of one of the peaks. Also, another point, the defect frequency must be inside the band gap. I hope this helps.