The tree is on the left side of the program.
If you click an item on the tree the editor for that item is shown on the right side of the screen.
Change the order of items in any section by dragging and dropping them on the tree. More information.
Right click on an item on the tree for a pop up menu.
Doing this on a scene shows this menu: 
The Tree Window
Right click on a chapter or scene to set how much of it you've completed. A small image in the tree shows this. E.g.
