Although I doubt there would be much of a difference between the two, fire towards the rear-door if you can, b/c thats the most direct way to extend the wavelength and send it to the front of the vehicle. Still, thats mostly speculation, in my opinion I doubt you'll notice a difference.
It make a difference, sometimes a very big difference. Generally, you will get more output with it firing at the tailgate, and reflecting back, as you will get a wave reinforcement effect. Generally Id say up for better SQ, back for better SPL, but not always. Only way to know for sure is try it yourself.
edit: btw SUV's dont have trunks. //content.invisioncic.com/y282845/emoticons/tongue.gif.6130eb82179565f6db8d26d6001dcd24.gif