We develop a general formalism to describe the dynamical behavior of an ensemble of two-level systems in a Fabry-Perot cavity. Our main result is a set of space and time-dependent, integro-differential equations for the slowly varying radiation and atomic variables, which we derive through a precise analysis of the slowly-varying amplitude approximation in the presence of counter-propagating fields. With the help of new and properly chosen variables we recast these equations in a form that makes their boundary conditions formally identical to those of an ideal Fabry-Perot resonator, and introduce in a natural way a modal structure even for systems with arbitrary mirror reflectivity. We derive simplified forms of these equations in the uniform field limit and within the more general single-frequency approximation. Finally, we extend our formulation to include driven systems such as optically bistable devices and the laser with an injected signal.