In version 2.4.0.2 we changed the default value of the setting Joe D posted from false to true so by default admins will use the /Data/Sites/[SiteID]/media folder instead of the /Data/Sites/[SiteID] folder as their root level folder. The root level folder for a given user depends on their upload permissions/roles.
Part of the reason we changed this is because the new feature for dropping images directly into the editor puts the image in whatever the root level folder is for the user. Therefore just be aware that if you do change it back to false then images that admin users drop into the editor will land in the /Data/Sites/[SiteID] folder which might no be the best place for it. Of course one can still use the dialog page to upload which gives full control over the upload location.
Hope that helps,
Joe