you definitely suffer from confusion but that's normal for someone new to this

if you use tunerPRO (not tunerCAT) at least use my XDF file. nothing else will do this ecm justice for a 'new tuner' (there are other versions for more advanced stuff) http://fbodytech.com/eex-tunerpro-definition/

bricking your ecm during a flash is a real risk. you should read the bin from your ecm a few times before writing it, as the commands are nearly the same but the risk is zero while reading (the worst case is you power your ECM on and off again by unhooking the battery). if reading succeeds without issues, writing probably will too, but if not, you're going to have to hit the wreckers for a new one or fix the old one with lots of very fine soldering.