How to write coupled mode equation of a given structure

Recently I am reading the papers in the field of PT symmetry systems. What I am confused is that in these papers, authors directly write out the equations describe the dynamics of the given systems( For example, in this paper http://arxiv.org/ftp/arxiv/papers/1103/1103.3389.pdf , authors put forward a honeycomb photonic lattice and they just write out the equations).
Now I am reading the papers about CMT written by Haus and Huang, but I still can not figure out how to write the equation describe the dynamics of a given structure.
So my question is that what I need to do so that I can give the coupled mode equations.

Thanks.