JCE has a global File Directory Path to for the images/files location. This is found in Editor Profiles -> Editor Parameters -> Filesystem. By default, this is set to the Joomla "images" folder, but it can be changed to any value above the Joomla root, eg: "files"

Each plugin / button that manages files or images also has a File Directory Path value, which if not set, defaults to the global value. For the Image Manager Extended for example, this is found in Editor Profiles -> Plugin Paramters -> Image Manager Extended.

You can therefore set a global value to apply to all plugins, and a value for each plugin. For example, you could set "images" for the Image Manager Extended, and "files" for the File Manager, and even "video" for the Media Manager.

The File Directory Path value can also contain variables, to create and use unique folders for the users, dates, etc. See - https://www.joomlacontenteditor.net/support/tutorials/editor/setting-the-file-directory-path