I had to enter my code on the square enix account management page. I had my CE code and did select service, then add platform and it asked for my code. After entering the actual CE code, not the pre-order code my standard account changed to CE account. I bought from Gamestop, if SE hasn't supplied people with an actual CE code in addition to the pre-order code I guess you have to wait till you get that code.

In summary my account showed standard account until I registered the CE code on the SE account management site here :
Account page