I sometimes use the end (6 inches or so) of another slightly smaller box, make a hole in the middle of it and push the (already bubble-wrapped) neck through. That way the guitar's supported in the centre of the main box and doesn't shift from side to side.
If there's any empty space left in the box I chuck in some loose bubble wrap or lightly-screwed-up newspaper.
And make sure there's plently of padding/reinforcement in the ends of the box, because they're the bits which will get bashed.