I had Justin tune mine when he was in town...I have not had to mess with it yet, but from what I understand...its fairly straight foward.
Get auto cal device.
Download free EFIlive software to your laptop.
Log data..ie full throttle,cruise etc.
Email Blackbear the files.
He will look it over and "fix" lags etc and couple them with BlackBears proprietary tune adjustments tailored to your desires. He will email back the new files to you.
You download the new files to your autocal.
Finally upload the new tunes to your truck using your autocal.
And then enjoy...