Mary, I guess you mean you have to enrol the cohort into the course via the enrolment method "cohort synchronisation"? And have to do that course by course? That should be possible via the "upload courses" mechanism (Moodle 2.6). However, the documentation is rather vague and/or a bug has not been resolved yet.
Enrolment
Enrol User's into category while uploading Bulk User's
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