Ok. With a texture map my recommendation would be to use ZAppLink.
First off, I assume you’re using polypaint? If not, you should be!
Then it’s simply a matter of selecting the subtool that you are wanting to paint and using ZAppLink to send it to Photoshop. You will now be able to use things like the Clone tool to copy from the other subtool (which will still be visible) to the new one. Photoshop’s other features will be available as well. In short, you’ll be able to get a perfect transition between the two subtools. When you return to ZBrush that will get added to the model’s polypaint, which you can later convert to texture.
If you still get problems after that, then they would almost certainly be due to UV issues. In which case no amount of texture-side effort will resolve the problem.