On tab Files Transfer you have the ability to choose any file, or folder to copy to the destination site.
On the left side table you may view all source site files and folders. You can browse within the folders and choose any file, or folder you wish to transfer.
On the right side table you may view all of the current destination files and folders. You can browse to any folder you wish. The folder showed here is the destination folder. For example if you wish to transfer some files/folder from the source site images folder, to the destination site folder images, then first you must browse in the images folder, then choose the files/folders you wish to transfer and hit button transfer.
In case you choose a folder to copy, and is not present on the destination site, then the folder will be created and transfer all it's sub-folders and files.
Remember that if you choose in general options to avoid overwriting existing files, then that will be the case!