Thanks for your review, but i think you has not understand exactly the specially jDownloads system and structure.
jDownloads created for any category a directory with the same name. When you will assign a file for many categories, you must upload it separately for every category.
This is the only way to have a clean folder structure in the same way as your categories.
That jDownloads is not easy to use is only your opinion. See the other reviews about this.
But i work on a complete new release and hope this is also perfectly for you...