The bay on the right is for the TCU, the bay on the left is (usually) for the Sirius receiver. Both of these are optional (Premium package, Sirius).
The Logic7 controller/amp is under the plastic cover (with the kleenex-box icon on it) on floor left-rear of the trunk. This is also where the CD changer goes, or the Sirius radio if you have the weird sept/06->march/07 configuration. Either of these requires a new left trunk carpet with a lump here.