Go to your "Manage Classes" page and click the class name for the class in which your student has created more than one account. Scroll down and select the student's multiple accounts (up to 2). At the top of the student roster, click on the "I want to..." menu button. Select "Merge selected duplicate student accounts" and click the "Apply" button next to it.
This will merge your students' multiple accounts and assignments. Students will only require one login username and password for this merged account.