You could always override a transcript grade in the Class Manager by clicking on the number of students in a particular section and choosing the override icon. Then you can enter the override information and save.
However, now you can complete the same process directly in a student record. To do this, navigate to the People tab and select a student record. Scroll to find the Transcripts tab, and click on it. Notice there is a new column, the Transcript Override column. Click on the cog. In the new window, enter the override data. When you're finished, click Save. The new override data is now visible.