What's worked for me is to put the frosted cupcakes on a very large plate and cover in plastic wrap. Push the plastic wrap in between the cupcakes though, and when the car moves around a bit they won't smudge against each other.
As for placement,
I like to put them on the floor in the backseat. The confined space doesn't allow them to move much.
And of course, be sure to drive carefully to keep them as perfect as possible!