All user-specific data is stored in in the XBMC home directory which, for a standard installation, is found in your windows users' application data directory, which is %APPDATA%\XBMC\. The UserData Folder, where your settings, thumbs and library files are stored is located in the UserData folder within this directory. Similarly, skins, plugins and scripts should be installed by the user into this directory.
XBMC will not alter this directory on an upgrade, so your data will remain safe between upgrades of XBMC.
