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The rules (1 days sick and 2 times late) are immaterial for your calculation because you do intend to reward those who are never sick and never late. The most simplistic way - just to show the system - is to say at each employee has 20 points (1 point = 1%) for time keeping & attendance. Each day missed costs 3 points and each time he is late it costs 1 point. At the end of the 6 months the perfect employe still has 15 points left and gets 15% of his bonus, or 75% of the bonus in this category.
You can convert this system to a monthly basis by adding the remaining bonus points for 6 months and divide the total into 6 (pay monthly bonus at average of past 6 months). For phase-in and new employees grant 10 bonus points for every month in which they were not eligible to earn demerit points.