Typically if the center console is getting hot enough to burn your leg when resting it, it probably is a problem underneath the car or hood area. It could be an exhaust leak, although normally you'll hear it, or it could be that a heat shield or insulation is missing.
If the A/C works upfront, but not in the back, it could be related to the heat issue above or the air getting into the rear A/C is not correct. I have not looked to see if there is a blend door that controls the rear A/C. Almost sounds like they could be related.