I went to the module (i.e. Management skills) and clicked course > enrolment methods. Then added 'course meta link' and chose the relevant qualifications (e.g. Level 3 in Business, Level 3 in Business IT). I then repeated this with the other modules.
Then, whenever I enrolled students onto the Level 3 in Business (or Business IT) course, it automatically enrolls them onto the correct modules.
The first time I had tried it, I had done it the wrong way around (adding the module courses to the qualification course instead of adding the qualification courses to the module course).