No, the Superchips modules do not work on TJs. They claim to, but they don't. They only work on 07+ JKs and JLs.
The HPTuner MPVI2 is the OBDII connector you need. With it, you can then download the VCM software suite (linked to on their website) for free. With that software, you then connect your laptop to your OBDII port, register the VIN number with the software, and then you have full access to the PCM.
This is where someone like Josh Pearl comes in. He sends you a base tune to install with the software, and then you drive around for a week or so while your AEM wideband O2 is data logging and collecting realtime data.
At the end of the week, you send that data log to him, he goes through it, and then he adjusts your tune accordingly. You do this for several weeks until your tune is dialed in perfectly. Each time you send him data from the wideband O2, that means he can fine tune your tune even more.
This is what we refer to as "remote tuning" since he can do it from anywhere in the world, and it's all done remotely.
Josh can walk you through the entire process as well, so you won't ever feel confused or like you don't know what to do next. It's actually very, very easy once you understand what's going on. This is the way remote tuners do it for any vehicle, not just our Jeeps.
I only recommend Josh because he comes highly recommend from Charles, and he has tuned a lot of these supercharged TJs, so he knows what he's doing.