The properties window at the bottom only shows the current selected link/package.
For mass changes you have to select the link(s)/package(s) and use the actions from rightclick context menu, there you can mass change the download folder.
In case you don't want JDownloader to use subfolders by default, just disable the rule, see
https://support.jdownloader.org/Know...ackage-feature
Please know that changes will only affect new added links.