Atom interferometers in optical cavities benefit from strong laser intensities and high-quality wave fronts. The laser frequency pairs that are needed for driving Raman transitions (often generated by phase modulating a monochromatic beam) form multiple standing waves in the cavity, resulting in a periodic spatial variation of the properties of the atom-light interaction along the cavity axis. Here, we model this spatial dependence and calculate two-photon Rabi frequencies and AC Stark shifts. We compare the model to measurements performed with varying cavity and pulse parameters such as cavity offset from the carrier frequency and the longitudinal position of the atom cloud. We show how setting cavity parameters to optimal values can increase the Raman transition efficiency at all positions in the cavity and nearly double the contrast in a Mach-Zehnder cavity atom interferometer in comparison to the unoptimized case.