We present the application of a method [Phys. Rev. E 76, 041115 (2007)] for deriving stochastic partial differential equations from atomistic processes to the morphological evolution of epitaxial surfaces driven by the deposition of new material. Although formally identical to the one-dimensional (1D) systems considered previously, our methodology presents substantial new technical issues when applied to two-dimensional (2D) surfaces. Once these are addressed, subsequent coarse-graining is accomplished as before by calculating renormalization-group (RG) trajectories from initial conditions determined by the regularized atomistic models. Our applications are to the EdwardsWilkinson (EW) model [Proc. Roy. Soc. London Ser. A 381, 17 (1982)], the Wolf-Villain (WV) model [Europhys. Lett. 13, 389 (1990)], and a model with concurrent random deposition and surface diffusion. With our rules for the EW model no appreciable crossover is obtained for either 1D or 2D substrates. For the 1D WV model, discussed previously, our analysis reproduces the crossover sequence known from kinetic Monte Carlo (KMC) simulations, but for the 2D WV model, we find a transition from smooth to unstable growth under repeated coarse-graining. Concurrent surface diffusion does not change this behavior, but can lead to extended transient regimes with kinetic roughening. This provides an explanation of recent experiments on Ge(001) with the intriguing conclusion that the same relaxation mechanism responsible for ordered structures during the early stages of growth also produces an instability at longer times that leads to epitaxial breakdown. The RG trajectories calculated for concurrent random deposition and surface diffusion reproduce the crossover sequences observed with KMC simulations for all values of the model parameters, and asymptotically always approach the fixed point corresponding to the equation proposed by Villain [J. Phys. I 1, 19 (1991)] and by Lai and Das Sarma [Phys. Rev. Lett. 66, 2899 (1991)]. We conclude with a discussion of the application of our methodology to other growth settings.