When I used to do bonus points, they would be awarded as a percentage of the marks you didn't earn on the rest of the assessment.
Eg, you earn 80 out of 100 marks on the main questions, you could earn 10% of the remaining 20 marks from a bonus question.
I liked it as a system as it disproportionately rewarded worse performing students who maybe had trouble with the main material but could offer some insights on the more conceptual bonus questions.