We study the coupling between photonic molecules and waveguides in photonic crystal slab structures using finite-difference time-domain method and coupled mode theory. In a photonic molecule with two cavities, the coupling of cavity modes results in two super-modes with symmetric and anti-symmetric field distributions. When two super-modes are excited simultaneously, the energy of electric field oscillates between the two cavities. To excite and probe the energy oscillation, we integrate photonic molecule with two photonic crystal waveguides. In coupled structure, we find that the quality factors of two super-modes might be different because of different field distributions of super-modes. After optimizing the radii of air holes between two cavities of photonic molecule, nearly equal quality factors of two super-modes are achieved, and coupling strengths between the waveguide modes and two super-modes are almost the same. In this case, complete energy oscillations between two cavities can be obtained with a pumping source in one waveguide, which can be read out by another waveguide. Finally, we demonstrate that the designed structure can be used for ultrafast optical switching with a time scale of a few picoseconds.