Hello Shruthy,

The marks you scored in your qualifying exam, that is, in your 12th are just a Criteria of eligibility in JEE main. They do nothing ,but make you eligible for the JEE main test. All the ranking is solely done on your performance in JEE main test. Though there are some private institutions which accept JEE scores for admission, not all of them, but some may use your 10+2 score for normalisation . But for NITs, IIITs, and GFITs this is not done. 

I hope this helps .

The ranking won't be done on the basis of the 10+2 score but then you should have secured at least 75% marks in 10+2 exam or be in the top 20 percentile in 10+2 conducted by the respective Board. For SC/ ST candidates, the qualifying marks in 10+2 are 65% or more.