1. If you want to upload just a single file you should use section File Transferring->Single File Uploading. Updating after uploading is available here.
2. To upload not a single file, but a folder, you have to use page I-Net Site Transferring->Folder Uploading trough FTP. Updating is available only as Professional DUGroup Options.
3. In last builds of v0.91 and in version 0.92 new method will be available: FTP Site Manager. You will have an opportunity to work with your remote FTP-site just like with local folder.