How to watermark all photos in a folder and its sub folders?
  

There is a check box on the toolbar above the thumbnail view called Recursive. By checking it, all images in folder as well as its sub folders are listed for watermarking.

When you batch watermark all photos recursively, the sub folder structure will be kept in the destination folder.

For example, you choose C:\MyPhotos folder which contains Folder1, Folder2, Folder3.... Your destination folder is D:\MyWatermarkedPhotos. You will have Folder1, Folder2, Folder3... in this destination folder.