There are multiple ways to do this automatically in jD. I will describe the one using FTP transfer and the use of manual initiation of the Auto Monitoring process.
First note that it takes time to create a Download so handling all of the items at once on a regular server means that one could exceed the PHP permitted time allowance. So dependent on the quality of your host server you should only do a few hundred at a time.
With regular files zips, docs, etc there is little to do but if you have an audio or video file then jD can make a preview which takes time. These previews are made once and stored. Similarly with image files jD can make thumbnails which also takes time. So the number handled automatically before running out of time may vary according to file type.
The root directory for the Categories (directories) and their Downloadable files is in the Joomla! root directory. It is a directory called jdownloads. Top level Categories are directories in the jdownloads directory. A sub category is directory in a top level category; and so on in a normal tree structure.
A Download consists of multiple parts; the foremost of these is the file that is to be downloaded. The files are is placed in the relevant directories (categories, sub-cats and so on) as appropriate. Other parts of a Download optionally include description, creator, licence, and many other attributes that are stored in the database.
If the file is an audio or video type then it can have a preview file. jD will use the audio or video file as the preview if one is not specifically added. If you have a large number of audio or video files then please check back with us.
If the file is an image file then jD can be told to automatically make a thumbnail version to be shown when users are viewing Downloads. Similarly if the file is a pdf then a thumbnail of the first page may be generated. In both situation the thumbnail making ability may be turned off in jD Configuration - Pictures tab - Thumbnail section. When using the auto monitoring facility it is recommended these features are turned off because of the time it takes.
jD fully supports the Joomla! permissions and view access features. If all your Downloads are downloadable by any user then one just has to set the Public User Group Permissions in the Component permissions to allow downloading. If however you have a mixture of public and limited access by User Group then your top level categories should be created manually with the correct Permission settings and view Access Level. The reason for setting up the top level items is that subsequent categories and Downloads will automatically pick up these settings from their parent. Should you be in that situation and need more help then first please consult the documentation athttp://www.jdownloads.net/documentations/category/access-controls-and-user-group-permissions
Should you still need more help on these aspects then please raise a separate topic as this is more helpful to other users and easier to identify.
Before copying any directories or files with FTP to either the jdownloads directory or to an existing directory in the tree rooted at jdownloads directory, please turn off
Auto monitoring in jD Configuration - Monitoring tab by selecting No in the 'Download Directory Monitoring?' field. Also check which file types you want monitored to be created as Downloads.
At this juncture you can populate part of the directory tree with directories (Categories) and Files using FTP or any other method. Would advise not be too ambitious. A little tedious effort is simpler.
The next step is to go to the jD Control Panel. On the righthand side there is a tabbed panel. Select the Status tab. You will see a link 'Check Download area now'. Click on it and you will see jD reporting progess.
You can then obviously repeat the last two steps until completion, but it may be wise to do a check after the first batch of Downloads have been created.