To define a question as extra credit, first define the rest of your key either by scanning a known good paper or toggling the dark circles. Then, on the extra credit question, press the 'i' on that questions row in the 'Edit Key' screen.
This will bring up the question detail screen and allow you to enter alternate answers. For the primary answer for this question, set the 'answer' to blank or some random letter and give it a point value of 0. Then press the '+' to add an alternate answer. Set this new alternate answer to the correct extra credit answer and git is a positive point value.
Overall, the point value of the quiz is based on the sum of the point value of the primary answers. If the point value of the primary point value is 0, then any point value assigned to the alternate answers is extra credit.