Spin-dependent optical potentials allow us to use microwave radiation to manipulate the motional state of trapped neutral atoms Phys. Rev. Lett. 103, 233001). Here, we discuss this method in greater detail, comparing it to the widely-employed Raman sideband coupling method. We provide a simplified model for sideband cooling in a spin-dependent potential, and we discuss it in terms of the generalized Lamb-Dicke parameter. Using a master equation formalism, we present a quantitative analysis of the cooling performance for our experiment, which can be generalized to other experimental settings. We additionally use microwave sideband transitions to engineer motional Fock states and coherent states, and we devise a technique for measuring the population distribution of the prepared states.