When you register your account, use the code to activate the account. After that is done you should have all content you are entitled to already enabled.
I believe you should receive two codes:

POL code: creates the account)
FFXI code: creates the first game content ID, enables all expansions, is used later on to create new character slots
I might be wrong, though. On older purchases you would receive a TON of codes. I have like 15 codes: (the first four came on the game box when I bought it

PlayOnline
Tetramaster (no longer in service, rest in peace lol)
JongHolow (also no longer in service. Japan only, PS2 only...)
Final Fantasy XI (This code is also used to make new chars without delete existing ones)
Final Fantasy XI - Rise of the Zillart
Final Fantasy XI - Chains of Promathia
Final Fantasy XI - Treasure of Aht Urgan
Final Fantasy XI - Wings of the Goddess
Final Fantasy XI - A Cristaline Prophecy
Final Fantasy XI - A Moogle Kupo'd Etat
Final Fantasy XI - A Shantotto Ascension
Final Fantasy XI - Visions of ABYSSEA
Final Fantasy XI - Heroes of ABYSSEA
Final Fantasy XI - Scars of ABYSSEA

The last 6 have codes that were mailed to me after I purchased (automatically) but they do exist.

So no wonder they would try to simplify the process. Imagine a person register that many codes the first time they try to play the game.