We study the coherent flow of interacting Bose-condensed atoms in mesoscopic waveguide geometries. Analytical and numerical methods, based on the mean-field description of the condensate, are developed to study both stationary as well as time-dependent propagation processes. We apply these methods to the propagation of a condensate through an atomic quantum dot in a waveguide, discuss the nonlinear transmission spectrum and show that resonant transport is generally suppressed due to an interaction-induced bistability phenomenon. Finally, we establish a link between the nonlinear features of the transmission spectrum and the self-consistent quasibound states of the quantum dot.