Aries makes a security setup. Kind of expensive but an option. I would post a pic but this app isn't allowing me to do so. You can google it.

 

Why do you still have your back seat in a 2dr., that wasting space.

 

well, to tell you the truth. I like throwing stuff back there (on the seat). Back when I had a 99 TJ I removed the back seat and put in a large full-range speaker box and built a deck around it. This time (2010 JK) I dont really want to change everything so much. I wouldnt mind a large amount of storage back there. But maybe later. I can always remove the seat later or fold it up if I needed to carry a lot of stuff. At the moment... All I need to keep in the jeep (that wont fit in underfloor cubby, behind the passenger-side tail light , the glove box and center console) is my metal detector case and a battery jump-box.

Plus... I kind of like sleeping on the bench seat (sometimes I need to for my job... dont ask). Also... seems a bit of a waste to take out leather seats.

 

Dirtymoney.....sounds like it's time for a dual battery setup for you. It'll allow you to jump yourself and it fits under the hood. That'll give you a little more room in the back to work with.

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I have a 2 (half doors) JK soft top. I have the 'Tuffy Security Products Tailgate Security Enclosure' and it works very well.
Tuffy 282-01 - Tuffy Security Products Tailgate Security Enclosure for 11-14 Jeep® Wrangler & Wrangler Unlimited JK - Quadratec

 

One of my first add-ons back in 2009....picked this up at the local WalMart for under $40.00. Fits perfectly in my 2-door with the rear seat flipped forward.








With the rear seat down I find that a few soft "tool bags" work well for storage. They conform better to the angle of the seat.

 

Here is an idea, its a little on the costly side but should work really well. SUV Cargo Caddy : Cabela's

 

The OP was asking for solutions for a 2 door with the rear seat in and NOT folded. I think I saw ONE solution that was way over priced for what you would end up with. I'm inclined to find some kind of a lockable tool box and just bolt it to the floor of my storage area.

 

I have the tuffy enclosure as I need a secure area to put stuff as I own a soft top half door. Works great and not overpriced for what you get (something that works and is secure). I could not find anything else for the two door.

 

If you are looking for a cooler that fits perfect behind the rear seat. Check out JP Cooler, I've been using one for 6 years and love it!

JPCooler - Soft sided coolers made for Jeeps, Boats, Rhinos, Trucks, and SUV's