Your welcome! It's entirely up to you on how you want to run your subs or just one sub. I think when getting into the SQ side of audio, most people rely on the equipment to most of the work to sound good, but in actuallity, it's the installer who needs to do the extra work for the highest SQ potential to be reached. When it come to the subs being in the rear of the jeep, facing them together will probably cause a phase problem that will need to be addressed, maybe by installing them at an angle from each other. But i would just recommend them to be faced forward or towards the rear. Running the subs at full tilt at 2 ohms or 4 ohms is again up to you. If any noise is introduced into the system, it will be because of the installer(example, not running the power wires and rca's far enough apart or not grounding correctly) has not properly installed the devices. The amount of noise that will be added by running in 2 ohms instead of 4 ohms will be inaudible to you inside your Jeep. Not to say that it wouldn't be audible if you went all out and sound deadened every single panel and ran the stereo with the engine off, you will probably still not hear the added noise.
A couple more questions,
Have you upgraded your headunit, or are you using a line-out-converter?
What type of power wires and rca's have you chosen?
Are you gonna sound deaden, or do you think the extra weight my affect your off road performance?
Sorry it took so long to get back, but I am on the forum all day, but you popped back on a soon as my old a-ss when to sleep! Lol, I still can't believe i go to sleep at 7.