If you wish to change the position of the boxes, you MUST click on the edge of the box (as marked in red in the screenshot below). The black arrow will then pop up. You can click on it and then drag and drop the box where you want to have it.
To delete a box, click on the "x" next to the error.
The same counts for the chapters on the left hand side. Simply click on the page or chapter you wish to move around and then the black arrow and "x" will pop up. Now you can drag and drop it to the position you desire.