When uploading your photos to ZenFotomatic through the 'upload' button, you can select up to 2000 photos at a time. If the desirable upload amount exceeds 2000 photos, you will have to upload in segments of 2000 photos.
If you wish select the folder with all the photos enclosed that you wish to process, you are able to drag and drop this folder into ZenFotomatic. However, if you wish to organise your photos into folders on ZenFotomatic, upload your folders in a zip file and it should do this for you with a folder directory to the left side. It will display as below: