When I owned my Jack Russell's they both traveled in dog crates in the estate part of the car but that hasn't been practical with the dogs we have now. We did try our little dog in a crate but she was terrified so we progressed to letting her ride loose in the estate. Being so small however she could get through just about any gap (even the dog guard) and therefore ended up sitting on the passengers lap where she now stays!
Our larger dog progressed from the estate part of the car to the back seat once he learned how to not only move the dog guard but pull the cord to lower the back seat allowing him to park his butt in between the kids. As a result we have removed the middle seat now so he can lay quite happily on the floor between them on his soft squishy quilt!