I think it depends on the year, but here is how it worked on my '04:
1) Inside the tailgate there is a bracket that it has a plastic cover over it that is held on with one screw. Remove it, and you'll see where the wires for the rear brake light plug into the contacts. If you unplug them, you can pull the wires through the tailgate. Note: there are two contacts inside the tub that become exposed when you remove the contact bracket from the inside of the tail gate. Cover them with tape or remove them too. A friend had a metal tool box sitting in the back of his Jeep that would bridge the contacts every now and then. He couldn't figure out why he was blowing fuses so often....
2) The brake light is attached to the rear tire carrier, there are four bolts that hold the assembly to the tailgate. You can remove it as a single unit.
3) Remove the rear license plate from the bracket and you will see the four bolts that hold the bracket to the tub. You can buy a flat version of this bracket at Napa or Kragen if you want to mount the plate on something other than the bare tailgate.
Another thing to think about is lighting the plate if you live in a state that requires it. Remember the wires you took off for the brake light? You could use the contacts to get power to a light by rewiring the contacts that attach to the tub to the tail lights instead of the brake circuit.
I did something a bit different with mine, but kinda the same idea: