Great question GhostSmoke. You sound like me, afraid to to move forward in fear of messing something up and not proceeding correctly. I too had a question along those lines. I know Shane Olson has a GREAT tutorial on the process of taking a hires model with polypaint out of Zbrush, redoing the topology in 3D Coat($99 aint…
In addition to Kodde's advice, you can bake the polypaint to auto-uvs in Zbrush and then transfer that do your actual uvs during the bake. Eat3d has a free tutorial covering that process: http://eat3d.com/free_zbrush_xnormal_pipe