The most straightforward way to do this is to construct a single unit cell and then stack it vertically. Do not stack it horizontally. Then you use periodic boundary conditions on the sides which will make it look like an infinite lattice. Then source it from the top and record S11 (reflection) and S21 (transmission).
Without getting into the details of the actual simulation package, that is about it. The next level of detail would involve representing the geometry of your photonic crystal more accurately and perhaps incorporating material dispersion. The next level of complexity after that is to source the lattice and record its response in a manner that best models the actual experimental setup you have to measure the same data.