HI, 

The aggregate percentage will be calculated according to the marks that you will get in the improvement exam. that is the marks that you will have in your final mark sheet.

Here is the eligibility criteria for jee mains and advance:

Eligibility for Admission to NITs, IIITs and CFTIs participating through Central Seat Allocation Board: Admission to NITs, IIITs, and CFTIs participating though Central Seat AllocationBoard will be based on All India Rank as explained above subject to the condition that the candidate should have secured at least 75% marks in the 12thclass examination, or be in the top 20 percentile in the 12th class examination conducted by the respective Boards.ForSC/ST candidates the qualifying marks would be 65% in the  12th class examination. 

thank you