Using a novel dual-beam readout with the generalized phase contrast (GPC) method, a multiple-beam 3D real-time micromanipulation system requiring only one spatial light modulator (SLM) has been realized. A theoretical framework for the new GPC scheme with two parallel illumination beams is presented and corroborated with an experimental demonstration. Three-dimensional arrays of polystyrene microbeads were assembled in the newly described system. The use of air immersion objective lenses with GPC-based optical trapping allowed the simultaneous viewing of the assemblies in two orthogonal bright-field imaging perspectives.