The self-organization of active particles on a two-dimensional single-occupancy lattice is investigated, with an emphasis on the effects of boundary confinement and the influence of an external mean fluid flow. The study examines collective behaviors, particularly the transition from a disordered phase to the formation of orientationally ordered patterns, and their impact on particle transport and flux. In the absence of fluid flow, confinement causes particles to accumulate near the walls, leading to clogs or obstructions that hinder movement, or to the formation of bands aligned with the channel. Although these bands limit the particles ability to freely self-propel, they still result in a net flux along the channel. The introduction of an external Poiseuille fluid flow induces vorticity, shifts the phase transition to higher alignment sensitivities, and promotes particle clustering at the channel center, significantly enhancing overall flux.