When you activate this add-on, the admin/instructor can manually enroll users/students to the course without having them go through the checkout process.
Once you have activate the Manual Enrollment add-on, navigate to the following location.
Masteriyo > Manual Enrollment
To enroll manually, click on the New Enrollment button on the top-right.
Basically, you will have two options available. The first one is to select the Course and the second one is to select the student. Once you have matched the course and the student, click on Enroll. The student will then be enrolled to the choice of the course by an admin or instructor.
To see all the student who are manually enrolled, you can go to the Masteriyo > Manual Enrollment. If you want to make any changes to the course, you can click on Edit.