You can change the page structure of the course by dragging pages to the desired location in the content section. If you want to move individual pages or entire page sections to sub-pages of another page, drag the desired page onto another. A small arrow icon indicates that the page contains subpages.
If you want to preserve the page hierarchy when moving pages, simply select the lowest level page in each page group before moving them—not every single page. If you select each page to be moved individually, they will be moved as pages at the same level.