All graphics and sound files you add to your web site are stored in the source file .wcg. This is also referred to as the graphic archive.
You can add new graphics and sound files directly to the web site's graphic archive. You can also remove files from the graphic archive that are no longer being used in the web site. These additions/deletions should not be done to the "graphics" folder that is created where you generate your course. Instead, from the tree/outline view, select Edit | Graphics Archive... This presents the files that will be placed into the site's main "graphics" folder when the site is generated.