As part of course editing in SIS you will find a checkbox on the data entry page labeled "Online Course Evaluation". If the course is a thesis, independent research, directed study, recitation, internship or other special type of course, it will not be evaluated by default. You can override the default by setting the 'Override Component LMS/EVAL' flag. 

Five weeks into the term you will need to run the "Course Evaluation Proof" query to review which courses you marked to be evaluated.

The video below details the steps Department Administrators should take to ensure that the correct courses are evaluated.