Modified theories of gravity have been invoked recently as an alternative to dark energy, in an attempt to explain the apparent accelerated expansion of the universe at the present time. In order to describe inhomogeneities in cosmological models, cosmological perturbation theory is used, of which two formalisms exist: the metric approach and the covariant approach. In this paper I present the relationship between the metric and covariant approaches for modeling $f(R)$ theories of gravity. This provides a useful resource that researchers primarily working with one formalism can use to compare or translate their results to the other formalism.