With PES6 Option File 2014, you don't need to manually update the player transfers. You only need to replace the "KONAMI-WIN32PES6OPT" file located at "My Documents\KONAMI\Pro Evolution Soccer 6\save\folder1". Try this article to learn more about PES6 Option File
To be able to use PES6 Option File 2014, you must first remove the old option file. Remove the option file will also mean to delete all your saved game.That means that all your league that in progress or saved match will be removed.