As long as it's in the same folder as your Morrowind.exe it should work.
There is no need to launch Morrowind from the FPS Opt.
As long as the FPS Opt is open, you can start Morrowind normally and it will work behind the game.
Make sure you're using http://planetelderscrolls.gamespy.com/View.php?view=utilities.detail&id=22, because version 2.0 has some problems.