Same problem here, don't know how this works :/
Don't see anything in game. Do you have to start a new game?
God, so blind -.-
Guys, when you cant find the Pre Order Bonus option:
you can find it in the game settings from the MAIN MENU. when you are alreade in a game and go in the game options you wont find it.
The problem, in my case, is that I have nothing in the "main menu", the one were you chose between classic game, Left behind or multiplayer while on my "Related content" tab every pre-order bonuses are reported installed.
I went to my downloads on my computer through playstation.com and and they give more of a description there than they do on the actual PS4 store, for the skins you have to beat the single player once, the 100 supplies are in MP and the single player upgrades were applied right away
I tried do redownload the pre-order bonuses via the playstation store website on my computer and same result, nothing show up in game anywhere.
Here are some screenshots :
As you can see got all addons reported installed but nothing in menu, nothing in game.
Well, that explains that, but I still didn't see the Joel and Ellie skins
Gotta beat the game first. All of this was made clear to us, folks