It depends which emblem and which product it was bundled with. For example, often there is an emblem added to cart as long as you purchase something. For this emblem, you'll receive a separate email shortly after your order confirmation. It will contain a link to download a pdf file, which will have the code. The second option is that the emblem is bundled with a purchase and in that case, arrives when the item is delivered. For example, I purchased the Destiny Comic Collection and the emblem code was inside the book.

You should have received an email from the sender "Bungie Store Digital Products." In that email, there's a link to download a PDF containing the code for your emblem. After you open that PDF, you copy and paste the code into your Redeem Codes portal on bungie.net: https://www.bungie.net/en/User/coderedemption.