Hello aspirant ! Let me to inform you that yes the class 12th board marks will definitely bother your admission in Iit Madras. For getting admission in Iit Madras the minimum percentage of marks in class 12 should be above 75% in the pcm group for general category students. If marks less than this then you won't be eligible for Iit Madras. 

Hello,

Your +2 marks will only be used for checking the eligibility of getting admission. According to latest rules you need score a minimum of 75% aggregate or be in top 20% of the board you have done class 12.

If you pass this eligiblity criteria you will get admission only on the basis of jee advanced marks.