With Jalbum you decide if you wish to work with real files or just links. Working with real files means that moving, renaming or deleting files within Jalbum will affect your files on disk. Doing it with links will leave your original files where you put them on your hard disk. (A link is indicated with a small arrow in the lower left corner of the thumbnail). Dragging a folder onto Jalbum will add a link to that folder. You can now safely delete that folder link without affecting any real files. If you however open a folder link, you will be taken to its destination which most likely contains real files. It is important to know that deleting those files will delete them physically from disk (and Jalbum warns about this).
Now with Jalbum 8 you can control-drag folders. This will create a folder inside Jalbum filled with just links to the files in the original folder. You can now safely do whatever you wish with that folder or its contents.