Plug it in and have fun.
Ensure you have the AFX USB drivers loaded, hook up the USB to the machine, then power on the AFX.
Set the Prefrences -> Audio/Midi -> Audio Input to AXE-FX II.
When creating a "New Track", select "Real Intrument", select your new track, click on the name and rename it appropriately, Select Show Track Info, and set the Input Source to be AXE-FX II. I usually run Monitor off as I monitor from an amp as I play.
There are no real modifications you have to setup except as to where to input your signal from.
Try recording your tracks from the AFX clean with no GB effects, then mix in volume and master track effects later when mixing your composition.
GB is everything you need to make awesome recorded music.