To sort the Order of Courses, the Courses need to have a sort order in Core. 

To change this navigate to: 
  1. Academics > Scheduling > Requests and Schedules> Classes > Departments & Courses
  2. Click Edit next to the name of a course you would like to edit the sort of
  3. In the sort order box, input the # that you would like that Course to display as
  4. Click Save & Close

In order to see the changes reflected, give the page a few minutes to refresh, and then open the page in an incognito/private browsing window.