This is tricky. I have actually carryed it across behind on a normal rack (NOT recomended) and has also twice carryed it vertically (sticking up over the top of the car- also not recomended). Now I use a trailer when transporting it with a car. I try to use a normal bike w trailer if I need to take it in a car or bus/train.
I have twice had a normal bike fall down on the roof of the car so personally I have almost stopped doing that.
I have decided (again) That I am FOR SURE going to finish my 20" detatchable longtail this year.