So - I use crates for puppies and just restrain the adult dogs with a 2 foot long leash that loops around the flap shaft in the baggage compartment. The short leash is just long enough to let them sit up and move around back there a bit - but keeps them back where they belong. I have transported many dogs as large as 60 lbs (one at a time) and this method works well. I remove the carpet from the baggage area and replace it with several layers of old bath towels followed by an old dog bed. So far, I have never had an adult dog have any kind of 'accident'. Getting them in and out of the baggage area is not as convenient as I would like - but it works. I lift them into the cockpit and then get them to walk under the back seat brace. When getting them out, it usually helps to have a helper standing on the ground to hand to dog to after you lift them out of the cockpit. There is a reason that 60 lbs is my max for a dog flight .
I had to carefully select crates that would fit in the baggage compartment for puppies (Petmate crates rated for up to 20 lb dogs). I have worked out a method so that I can actually get 4 of these in the plane at once if I remove the passenger seat - 3 if I don't. I have actually hauled as many as 13 puppies at one time using this setup.