I am also in process of doing same thing. I believe you are correct (two wires not used). If you ignore the center (common) wire, current rating has to be half of rated value (since resistance is double). If you ignore the other ends wire, current rating is as rated. I believe there's some info at Gecko site on this matter but let the CNC Guru confirm this.
My question, running unipolar as bipolar means two phase are energise same time (more torque). Doesn't this means the heat to be dissipated is doubled? Is motor heating something I should worry about?