At the moment, if you have a Legacy/1.0 account and bought the physical PC version CE for ARR, there is no way to redeem your code without creating a new service account. Apparently this was mentioned in a Letter from the Producer, 9 posts in on a topic about that letter on the forums and on the Beta forums and SE is taking a stance of "Well if you missed that info, too bad."

There have been a few topics on this:
http://forum.square-enix.com/ffxiv/t...al-CE-purchase
http://forum.square-enix.com/ffxiv/t...-a-1.0-account

There are a few others floating around, but those have been the 2 most active.