A practical computational scheme based on time-dependent density functional theory (TDDFT) and ultrasoft pseudopotential (USPP) is developed to study electron dynamics in real time. A modified Crank-Nicolson time-stepping algorithm is adopted, under planewave basis. The scheme is validated by calculating the optical absorption spectra for sodium dimer and benzene molecule. As an application of this USPP-TDDFT formalism, we compute the time evolution of a test electron packet at the Fermi energy of the left metallic lead crossing a benzene-(1,4)-dithiolate junction. A transmission probability of 5-7%, corresponding to a conductance of 4.0-5.6muS, is obtained. These results are consistent with complex band structure estimates, and Green's function calculation results at small bias voltages.