I just ordered my autotap. Unlike the ls1 engine, you can't change the values of the ecu with the autotap. Currently the only thing that you can adjust your fuel system with is the apexi AFC. YOu can adjust your fuel and ignition using the Greddy emanage. These are all piggy backs. Turbo xs is working on an piggy back system too and mopar is coming out with a remap of the stock computer.
All Chrysler ECU's are flashable. But Chrysler is very good at keeping them secret. The dealership will be able to flash the computer using the OBDII port, when the upgrades come available. Hopefully companys like Superchips, Hypertech, and Street and Performance will come out with something as they have done with the trucks.