First, I don't think this can be done from your computer with the PC3 disconnected and on battery-pack. You need to have your computer connected directly to your PC3 and your PC3 installed on your bike. That being said, the process is so simple that it sounds hard, so DynoJet put an on-line learning file on its website. There's a link to it in the Popular Mods topic (and there's a link to Popular Mods in my signature picture below). Look under ECU in Popular Mods.
Also you can go to: http://www.powercommander.com/powercommander_iii_usb/powercommander_general_downloads.aspx
See Item #10 and click on it for the tutorial. Its a one minute adjustment. I might sound like a broken record but read everything and also make sure before you set zero% or 100% that:
- All 4 spark plugs are clean and gapped.
- Air filter(s) are clean.
- WARM idle is set to 850~950 rpm preferably using the PC3 software for ease.
BTW you seldom need to set 100% throttle. The materials will explain why, and when.