Stock is "uncorrected" - so the default settings should have you running at stock.
After it is installed and before starting the engine, set the following:
- Set VTEC control to off.
- Put the NEO in Pro Mode.
- Set the Neo for 6 cylinders
- Set the throttle sensor characteristics (arrow pointing up and to the right for a Supra), the voltage for the TPS should be 0 when closed and 5 when at wide open. If you don't' see these results, your TPS needs to be adjusted.
- Set the airflow sensor to Karman
That should be all you need to do. Start the car up and it should run normally. If it does not check your wiring carefully. A properly installed piggyback with all settings at zero correction should not affect how the car runs.