Normally the FCK/CK online editors rely upon their own file system, which you can set up below /pictures/upload/. There you can make your own folder system and save your uploaded files. The editor will then be able to make use of them, offer them for download or for being displayed.
The CMS on the other hand has its own file system accompanied by the possibility to recalculate picture by a given size or means for activating theLightBox/SlimBox feature. This isn't possible when using the picture embedding feature of FCK/CK.
Files from the CMS file center can be placed directly within the text box of the FCK-editor. There is no need to make use of any CMS content part (CP) for single files. Just by clicking the button “search server” the “filebrowser” of the CMS is called, where you can select the appropriate files.
These files are saved automatically into /filearchive/ by the CMS, secured from direct access from outside for security and copyright reasons. While inserting a file into a text the file download.php is activated which then in turn will make it avalable for being displayed or for offering it for download. (pictures in turn will make use of the fileimage_resized.php).
Now the file download.php will be autom. used for download the selected file.
Now the file image_resized.php will be autom. used to show the selected image.
Have a look too: WYSIWYG (F/CK) image resize
The folder /filearchive/ can stay protected.