The left hand side of this area represents files on your local computer. At the top, your directory structure is displayed. Below, files in the currently selected directory are displayed.
You can click on a file or folder with your mouse, (left button), and then drag it to the right area of the window to upload it to your server.
To upload multiple folders or files which are not in a continuous list, hold your keyboard's Ctrl key down and click each file and/or folder you wish to upload, then drag and drop them in the usual way.
Be sure that you've navigated to the proper location on the remote server before dragging files over to the remote server.