We describe a method for evolving the projected Gross-Pitaevskii equation (PGPE) for an interacting Bose gas in a harmonic oscillator potential, with the inclusion of a long-range dipolar interaction. The central difficulty in solving this equation is the requirement that the field is restricted to a small set of prescribed modes that constitute the low energy c-field region of the system. We present a scheme, using a Hermite-polynomial based spectral representation, that precisely implements this mode restriction and allows an efficient and accurate solution of the dipolar PGPE. We introduce a set of auxiliary oscillator states to perform a Fourier transform necessary to evaluate the dipolar interaction in reciprocal space. We extensively characterize the accuracy of our approach, and derive Ehrenfest equations for the evolution of the angular momentum.