Molecular mechanisms of electrophoretic deposition (EPD) of poly(3-decylthiophene) (P3DT) molecules onto vertically aligned cadmium selenide arrays have been studied using large-scale, nonequilibrium molecular dynamics (MD), in the absence and presence of static external electric fields. The field application and larger polymer charges accelerated EPD. Placement of multiple polymers at the same lateral displacement from the surface reduced average deposition times due to "crowding", giving monolayer coverage. These findings were used to develop and validate Brownian dynamics simulations of multilayer polymer EPD in scaled-up systems with larger inter-rod spacings, presenting a generalized picture in qualitative agreement with random sequential adsorption.