Khan2Canvas has the ability to mark assignments as missing in Canvas if the due date of the Canvas assignment has already passed. However, when scores are marked as missing, by default they have no score associated with them. You can adjust your Canvas gradebook settings to automatically assign a percentage to missing scores.
Open Canvas and navigate to one of your courses. Click on Grades on the left hand side.
In the upper right hand corner find the gear icon and click on it.
Check Automatically apply grade for missing submissions
Fill in a percentage you would like students to receive for missing assignments.
Click Apply Settings at the bottom.
You will need to repeat this process for each of your Canvas courses.