It doesn't matter where you bought the first code or any code there after. All codes get applied to your Square Enix account. I personal think it's just easier to buy directly from SE because they are the source. Some people buy the physical package so they will go to gamestop or other locations.

The only think to keep in mind is what region is the code for and what verison your using. I actually have access to all platforms on my single account and can log in on anything that runs the game.