You need to talk to the shuttle selector person on the ship. Easy to find on the lockbox ships and shuttles, but its by the teleporter pad on the Engineering Deck.
Awesome, I found it. Thanks starkoas. In case anyone else is wondering, when you go to the engineering deck on the standard bridge, go all the way to the back and to the right, and you should see a ship selector icon on the map. That is the guy you need to talk to.
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