You need to register the 12 digit code that came with your game into the redeem code function of the PSN Store, then place the disc in the machine and start the game up. You'll go through a process similar to the pre-order process where you agree to terms again and confirm that you're adding that code's features to your pre-existing service account.

(Make ABSOLUTELY sure you do not select to start a new service account, unless you're wanting to start over from scratch and lose any progress and characters you've made)