This topic only applies to the legacy Windows Uploader mode and is for reference in legacy systems only. You will likely use the newer (and default) Web Uploader mode in production instead, and can safely skip this topic.
UploadZen lets you upload entire directory hierarchies including all (or only certain) files and sub-directories by simply marking a directory for upload.
To mark a directory for bulk upload, you can either navigate to it by clicking the Change Folder button, then selecting from the Change Folder drop-down menu the appropriate Mark entire folder contents (files and sub-folders) for upload menu item...
... or you can first select the folder(s) inside the local file navigation area and then from the context menu select either the Mark selected folders, their files and sub-folders for upload menu item or the Mark files and sub-folders of selected folders for upload menu item. (The second menu item will place the files and sub-folders directly into the currently selected Document Library target folder, the former will re-create the folder inside the currently selected Document Library target folder, then place the files and sub-folders inside that newly created folder.)
Once you have marked all folders for bulk-upload, click the Upload Files button to initiate the bulk-upload. Each directory will be ZIP-compressed in its entirety (in memory) for transfer:
UploadZen then uploads the in-memory ZIP archive to SharePoint where it will be extracted into the currently selected target Document Library folder.
Sometimes you want to put together a number of related files in one ZIP archive for uploading. UploadZen saves you the step of manually compressing files into a ZIP archive with an external tool; instead, you can simply select the files and tell UploadZen to compress those files into a ZIP archive which to upload in place of the individual files using the context menu:
This will put a single item (with a prefix [ZIP] and the names of the included files) into the Local Files Marked for Upload area, representing the dynamic ZIP archive that will be generated automatically once you start your upload:
As soon and as long as you have at least one ZIP archive marked for upload — whether an existing archive file you selected from your file system, or a dynamic ZIP that UploadZen will generate as described above — you will find check boxes next to these ZIP archives in the Local Files Marked for Upload area, as demonstrated in the screen shot above. Only tick the check boxes of those ZIP archives you want to extract into the currently selected target Document Library folder. This extraction will happen on the SharePoint server immediately after the ZIP archive has been fully uploaded.