We analyze coupled optical defect cavities realized in finite one-dimensional photonic crystals (PC). Viewing these as open systems, where waves are permitted to leave the structures, one obtains eigenvalue problems for complex frequencies (eigenvalues) and quasi-normal modes (QNM) (eigenfunctions). Single-defect structures (PC atoms) can be viewed as elementary building blocks for multiple-defect structures (PC molecules) with more complex functionality. The QNM description links the resonant behavior of individual PC atoms to the properties of the PC molecules via eigenfrequency splitting. A variational principle for QNMs permits one to predict the eigenfield and the complex eigenvalues in PC molecules, starting with a field template incorporating the relevant QNMs of the PC atoms. Furthermore both the field representation and the resonant spectral transmission close to these resonances are obtained from a variational formulation of the transmittance problem using a template with the most relevant QNMs. The method applies to both symmetric and nonsymmetric single and multiple-cavity structures with weak or strong coupling between the defects.