To order your courses on a report card you must set the Report Sequence Number or SeqNo field.
Schedule TT > Courses ST > Field Set: Report Card Field Set > Look at the SeqNo field.
0 is the highest priority, it will be at the top of the list. So leave your prefered top course as a zero and set the others to 1 or 1,2,3,4 etc if you want them in specific orders. Courses with the same SeqNo appear to order alphabetically on the report card.
You can mass update the Report Sequence Number. You can also use the Modify List option to change each individually.
It appears you are able to do this before or after preparing grade input.