Hi Rebecca,
If you're doing a SIS Import, your course has a required SIS ID for each course. You can use "sis_course_id:SIS ID" instead of the canvas-assigned internal ID to retrieve courses.
For example, our SIS ID format for courses is something like this: TST_100_001_U2015, and it's URL in Canvas may be
your_institution.instructure.com/courses/1527386
This is equivalent to saying
your_institution.instructure.com/courses/sis_course_id:TST_100_001_U2015
This works in API calls as well.
Not sure if this works for your situation, but we have not needed to store internal Canvas ID for our use at the institution. Also the internal Canvas ID changes when course gets reset, so you'd have to know to re-get the ID when that happens.
Hope this helps,
Kumi