I just today pre-ordered the Collector's Edition from Game Stop and there was nothing on the receipt about a code or anything that gives me any indication where I can tell me account it really was a pre-order.

Will I still get all the pre-order benefits for pre-ordering from Game Stop? How do I make sure I get everything I should be getting for pre-ordering from there?

Gamestop is unable to provide the preorder codes anymore, because they thought they were just Closed Beta codes, so their system won't give them out anymore.

You will not get any preorder perks without it. So here's what you do. You take a picture/screenshot/etc of your receipt from where you preordered from Gamestop. You contact EME's support, and give this picture/SS to them, and ask if they can help put the preorder perks on your account since Gamestop couldn't give you a code. They will. Then you'll be all set!