My take on the progammer tools like EFI...I may be wrong or things may have changed...I'm too lazy to go out and read through all the stuff again.
THe programming tools like EFI and others are used to edit the parameters in the PCM/ECM to modify fuel delivery, change the R&P value, change tire size, adjust cooling fan temps, adjust auto trans shift points, adjust or delete torque management, edit or control various emissions related functions, edit or remove certain trouble codes, allow for larger injectors or other "hot-rod" type changes...ie camshafts...etc, allow for certain adjustments to electronic theft control, allow for changes from auto to manual trans. Basically the ability to edit or remove just about anything the PCM / ECM controls or has hard data loaded in it that it assumes is right.
Good example...when you change from 3.73 to 4.11 or lower...the PCM/ECM has no way to know that and its programming assumes the stock ratio....same way with tires ..etc.
I don't recall but I'm not sure if the programming tools also come with diagnostic displays too or the ability to clear codes and see all the data in real time, it would make sense that they would.
The best course of action is to get up with a local guy that does programming if such a person is local to you...and as noted.
I assume there is some programming when you put that supercharger on the truck? Is the engine entirely stock with stock transmission and all electronics present just like it rolled off the dealer lot...exhaust stock...etc?
Surf around on those web sites.... avg guy does not just pick up a fully functional programming software suite and be off and running with it, even in a matter of a months...in my view. If you are going to take that route...you might as well get on ebay or other source and buy a few spare PCMs that match your donor vehicle from where the engine came from.