Now it's important that your mesh was unwrapped before taking it into zbrush.
Basically, after importing the low-poly mesh into zbrush, I went into Tools > Geometry Turn Smt (smooth) OFF, then hit the Divide button a bunch of times - I usually aimed for 6 or 7, but it will vary depending on how dense your mesh was to begin with.
This leaves the model looking faceted, and doesn't smooth/distort the UV unwrap any. It's kind of a pain to paint on it since there's no representation of smoothing groups, but this is the best way to make sure your texture will be an accurate match to the actual lowpoly mesh.
Then go down to Polypaint (also under Tool) and click Colorize. After that, you can paint directly onto the mesh.
When you're done, click Texture Map (also under Tool) and click New From Polypaint. Then click the Clone Txtr button, and it'll copy your texture into the Texture menu and you can export it as a psd file.