Do you mean Pyblish is setting/altering the PYTHONPATH for you? Or that you when you add Pyblish to your PYTHONPATH, it isn't getting picked up?
To add Pyblish, we first need to figure out which install you are running. If you are using the recommended distribution for your platform, which seem to be Windows (looking att he
% symbols) and should be Pyblish for Windows then you should find a
/pythonpath subdirectory within that install which is what you are meant to add to your PYTHONPATH.
Try this, from a console on Windows.
$ set PYTHONPATH=c:\path\to\pyblish-win\pythonpath
$ set PYTHONPATH=c:\path\to\pyblish-win\lib\pyblish-x\integrations\maya;%PYTHONPATH%
$ c:\program files\autodesk\maya2016\bin\maya.exe
This will replace anything you currently have on your PYTHONPATH temporarily, and launch Maya with its Pyblish integration.
Within Maya, try importing Pyblish.
If that works, have a look in your file-menu for a new "Publish" option.
Let me know how it goes!