I had EFi for a bit.

Return to stock, don't start the rig but do what the prompts say.

Once it tells you it's finished, remove the key for a few seconds, then apply the patch over the stock tune.

As mentioned, have a charger hooked up, so you have no loss or corruption file when flashing both to the ecm.

You are correct on getting every code to man to pop up if you start it on "return to stock."

I tried it, but nothing happened; use Autocal to clear all DTC'S

Why you return to stock is so whatever is done to the ECM brings it back to Mopar spec, which the custom tunes "patch" is configured to run correctly.