To use Runestone Pair Programming support, turn it on and off for your course whenever you want in the Instructor Page of your custom course. Click on the Admin tab and then Course Settings button and check or uncheck Allow Pairs as needed.
When Allow Pairs is checked off, the Active Code windows will have a Pair? checkbox at the top like below. If students check those, they can type in the username of their partner to connect their code in the database. Whenever either partner hits the Save&Run button, it will be saved for both partners. If the other partner clicks on Load History, the shared code from their partner will show up. A comment gets put into the program to indicate the partners. When you are grading, look for this comment. Grades are separate for each partner.