In a multi site installation site specific files are stored on disk under webroot/Data/Sites/[SiteID]/
beneath this folder are folders for specific things including shared files, skins, gallery images etc, so there is file system isolation between sites. In the case of shared files the friendly name of the file and other attributes are stored in the db.
When a new site is created, its initial skins come from webroot/Data/skins and are copied to webroot/Data/Sites/[SiteID]/skins, this way any custom site specific skins are not shared unless they are put in the /Data/skins folder on purpose.
Hope it helps,
Joe