To subtract points from a specific assignment, like late penalties, you can enter a score like "42-5" or "18-10%". See Scores.
To start all students with 100% then subtract points for each penalty — like a P.E. class where students lose points if they don't suit-up or participate — you need to define at least two :
1. First create an assignment to start everyone with 100%. It can be worth any number of points. Give everyone full credit (the Fill Blanks menu is a shortcut for that). Title the assignment something like "Baseline". You may want to check the "Hide" checkbox so students don't see this on their grade reports.
2. Then create another assignment titled "Penalties" or something like that. Set the "Input as" menu to "Extra Credit Points". (You'll actually be giving negative extra credit points, so it will lower the grade, not raise it.) Check the "Independent Study" checkbox so it doesn't appear on grade reports for students who have no penalties.
3. To give a student a penalty, give them a negative score. For example, if the baseline is 100 points, and you give a score of -5, that lowers the grade to 95%. Or if the baseline is 20 points and you give -1 points, that leaves 19/20 = 95%. You may type Comments to indicate the date and/or reason for the penalty.
4. To give a second penalty, you may use the same assignment and lower the score even more, like -10 or -2. Or you may create a new negative extra credit assignment each week or whatever.
These penalties can be the entire grade, or just part of the grade if you use Categories.
See also: Attendance Grades