You may want to apply points for things that can't be graded by Mimir Classroom's auto-graders. More subjective or preferential coding practices like comments, naming conventions, and more can be measured using rubric items on Mimir Classroom.
A rubric item works similarly to an additional test case - you set how much the grade is worth and the total score is updated accordingly.
For example, if we have an automated grade worth 5 points and a rubric item worth 20. The total grade for this assignment would be 25 points.
Late penalties apply to rubric items, so if your student has a 20% late penalty, and you give them 5 points for their manual grade, their final grade will only be increased by 4 points.
In addition to a rubric items, you can add a "Score Modifier". This is a flat modifier to the students final score which is unaffected by late penalties. This can be useful for dealing with special circumstances.