You will have two codes, one for the preorder items (early access, cait sith minion and moogle hat) then you will get another when you pay off the order with the actual game registration. You will NOT get the game code until you have actually paid for the game. They would not give it to you on preorder, then let you cancel and use the code to register the game. Hope that helps.
All well and good if you ordered online from SE. I actually went into a Gamestop and preordered. There will have to be a system in place for people with early access that ordered from other sources.
You should have got the pre-order code from Gamestop at the time of pre-order. It should be on your receipt. If not, someone screwed up and I'd contact them ASAP to find out what happened. For future reference, when pre-ordering games at physical locations, always make sure you verify where your code is. 9 times out of 10, it should be printed on the receipt. If it's not, it's probably due to the clerk screwing up somewhere when ringing up the order or they simply ran out. Either way, I would call it to their attention immediately, before leaving the store, as that would be the quickest and less painful. Unless, of course, you don't care about the pre-order items, then by all means, ignore this.