Non-portable installs behave like a normal Winamp installation, where everything is stored in your user folder (winamp.ini, ml related stuff), which is what I referred to as "it"
Portable installs have those settings within the installation folder (although 3rd-party plugins are disabled, which isn't the case for Non-portable installs), as you can then easily have WACUP on the go on a flash drive, hopefully this makes it a bit more clearer