Hi Tyler,
I have a 2-seat plane, and putting a crate in the baggage area is what I do. I'm not sure what the dimensions of your area are, but I found that I needed to get 'pop-open' type crate that would somewhat conform to my baggage area to be able to transport larger dogs. Something like this:
http://www.islandrentalservices.net/car ... etcage.jpg. The downfall is that the crate really should be washed after each transport. So, I cut out the metal loops and sewed on some cloth or velcro strips to the crate to be able to secure the metal loops back in. That way the cloth can be tossed in the wash machine.