We continue our earlier work [Ana Maria Rey, B. L. Hu, Esteban Calzetta, Albert Roura and Charles W. Clark, Phys. Rev. A 69, 033610 (2004)] on the nonequilibrium dynamics of a Bose Einstein condensate (BEC) selectively loaded into every third site of a one-dimensional optical lattice. From the two-particle irreducible (2PI) closed-time-path (CTP) effective action for the Bose-Hubbard Hamiltonian, we show how to obtain the Kadanoff-Baym equations of quantum kinetic theory. Using the quasiparticle approximation, we show that the local equilibrium solutions of these equations reproduce the second-order corrections to the self-energy originally derived by Beliaev. This work paves the way for the use of effective action methods in the derivation of quantum kinetic theory of many atom systems.