it is something with your theme, however I need to check the theme code to find the issue, please give me temporary wp-amdin login info in a private reply.
I didn’t understand your attached screenshots However you can set default upload location editing download-manager.php , line #31 define('UPLOAD_DIR',$d.'/uploads/download-manager-files/'); .
now, you need to use [audio_player] tag with page template to show play list, but from next update regular [file_list] tag with have play button too. And you also need to activate individual download from page settings in add/edit package window, more details about templates are here http://www.wpdownloadmanager.com/doc/templates/
Add additional condition in line 409 $cat->count > 0, but problem is if you do that, that also will hide the category and it sub cats, and sub cats may have packages
In your first reply, you edited core plugin code, but if you update plugin code will be erased, So if you use this hook wdm_before_fetch_template and place the code in somewhere else like themes functions.php, your changes will there even after you update plugin. The hook usage are here http://www.wpdownloadmanager.com/doc/filter-reference/wdm_before_fetch_template/
