There are two places on the Admin Course Materials page where you can change the order in which course material links appear on the Course Materials page.

To change the order of course material links that exist outside of folders, click the Reorder Materials link on the upper right of the page, next to the Add Materials link.

To change the order of course materials links that exist inside of a folder, make sure that the folder is expanded (i.e. the folder icon to the left of the folder name should show an open folder with a minus sign to its left), or else you will not see the Reorder Materials link. If the folder is collapsed, click on the folder icon to expand it. Click Reorder Materials link below the gray folder title bar.