Courses and course formats

I have been using Moodle for about a year now and have been having good luck with our current set-up.  Basically I have all of my main courses set-up and students are enrolled based on a group/cohort so that I can filter everything as needed for reports, gradebook, etc....works great.

Now I am trying to link our testing software (Examplify) to Moodle but it is getting confused because it can't recognize groups and only the class.  While that shouldn't be an issue it does become one on the testing side as anything posted to a course is available to any in that course and I can't filter it to a specific group.

Have been thinking of setting up, what I would call is a master course, so that anything we want the students to see would be there and would only require one spot to be updated if anything changes.  Then I would set-up another "course" specific to that group of students.

How do I link them so they don't see the two courses and can the gradebook in the master course pick up marks from the sub-course?

Or does anyone have any suggestions of a better set-up?  I don't want to get into just duplicating the course over and over as I feel that would be an issue pertaining to consistency of materials from one to the next.