You can enroll your students in more than one course on CodeHS by going to "Manage Course Enrollment" from your section page.
After you've selected "Manage Course Enrollment", you can choose which courses you would like your section to be enrolled in. Below you can see that Intro to CS 2nd Period is enrolled in both Intro to Computer Science (Golden) and Intro to CS in Python (Rainforest).
The Main Course should be the course that you want your class to be automatically taken to when they log into CodeHS. Make sure to press "Save" to save your changes.