There is a new Quadratec Cargo liner for the 2011-2012 JKs. I Just put one in my 12 2dr but I dont have the sub so I didnt have to cut it out but Im liking it way better than the carpeted mat Jeep put in mine.

 

The OP asked about the 2 door, not the 4. The answer is yes, it covers the the whole back when the seats are out.

 

My new Quadrated catalog lists the cargo liner for 07-11. I have the Rugged Ridge cargo liner (same as Quadratec) in my 12 JKR. I don't know if the sub is the same as the 11 but if you want the liner to fit right at the front of the sub you will not get it to fit tightly if you follow the cut exactly. The cargo liner was exactly the same as the Quadratec cargo liner in my wife's 08 JKUR with the sub and it is a nice fit around the sub. The 08 sub and 12 sub are not the same. The 12 has the power outlet on the left side of the sub and the bar going into it to keep the tailgate open.