Here is what is happening:

1) You have a legacy account and are automatically granted a free title of the game
2) With that free title you get a free 15 day subscription, and whatever other bonuses are with that depending on how long you subbed.
3) The only way to upgrade that service to a collector's edition is by paying for the 19.99 upgrade fee.

If you bought a digital/physical collector's edition through any other means you can't upgrade the legacy account, you would have to add another service account. I bought my digital collector's through GameStop and on the moogle station there is no where to enter in that code. If you bought the digital collector's edition I would highly recommend that you try to get your money back from where you bought it and just pay for the 19.99 upgrade fee, that gives you the in-game bonus items. The physical copy of the collector's edition through Square-Enix also can not be added to the legacy service account.