Eggsish: You have to finish the map to keep the skull. You can quit right after you found a black box, but if you quit when you picked up a skull it will reset and you'll have to do it all over again.
And I recommend finding the skulls and black boxes on easy so you don't have any trouble completing the map.
not sure thats right as i just went back and replayed the one with killing 750 infections - found the skull, resigned the game and it kept it.?
Maybe it wont work on a level that you haven't finished yet (playing through first time), but if you are replaying it then it will keep it?