Each affected creature's owner chooses whether to put it on the top or bottom of their library.

Every player gets to know whether a card is going to the top or bottom of any library.

However, if a player ends up putting multiple cards on top of their library or on the bottom of their library, either because a creature they owned but didn't control was rejected along with one they controlled or a rejected creature they owned was comprised of multiple cards (e.g. a mutated or melded permanent), other players don't get to know the relative order of those cards.