The coherent flow of a Bose-Einstein condensate through a quantum dot in a magnetic waveguide is studied. By the numerical integration of the time-dependent Gross-Pitaevskii equation in the presence of a source term, we simulate the propagation process of the condensate through a double barrier potential in the waveguide. We find that resonant transport is suppressed in interaction-induced regimes of bistability, where multiple scattering states exist at the same chemical potential and the same incident current. We demonstrate, however, that a temporal control of the external potential can be used to circumvent this limitation and to obtain enhanced transmission near the resonance on experimentally realistic time scales.