We analyze the resonant linear and nonlinear transmission through a photonic crystal waveguide side-coupled to a Kerr-nonlinear photonic crystal resonator. First, we extend the standard coupled-mode theory analysis to photonic crystal structures and obtain explicit analytical expressions for the bistability thresholds and transmission coefficients which provide the basis for a detailed understanding of the possibilities associated with these structures. Next, we discuss limitations of standard coupled-mode theory and present an alternative analytical approach based on the effective discrete equations derived using a Green's function method. We find that the discrete nature of the photonic crystal waveguides allows a geometry-driven enhancement of nonlinear effects by shifting the resonator location relative to the waveguide, thus providing an additional control of resonant waveguide transmission and Fano resonances. We further demonstrate that this enhancement may result in the lowering of the bistability threshold and switching power of nonlinear devices by several orders of magnitude. Finally, we show that employing such enhancements is of paramount importance for the design of all-optical devices based on slow-light photonic crystal waveguides.