Make sure they loosen the strings. It really helps if its in a hardcase. If not, just do the best you can with a gig bag or whatever they have. Keep the headstock and the edges protected from the edges of the carton that are going to be dropped on the ground.
Guitar Center whores out the cases separately so they can advertise a lower price on the guitar
. If the guitar is suppsoed to come with COA or any paperwork at all, insist that you get it before you pay them.