as u can read in this website: http://jee.iitd.ac.in/eligibility.htm
Candidates belonging to GE, OBC and DS categories must secure at least 60% marks in aggregate in their QE. Whereas, those belonging to SC, ST and PD categories must secure at least 55% marks in aggregate in the QE.
The percentage of marks awarded by the Board will be treated as final. If the Board does not award the percentage of marks, it will be calculated based on the marks obtained in all subjects listed in the mark sheet. If any Board awards only letter grades without providing an equivalent percentage of marks on the grade sheet, the candidate should obtain a certificate from the Board specifying the equivalent marks, and submit it at the time of counselling/ admission. In case such a certificate is not provided then the final decision rests with the Joint Implementation Committee of JEE-2010.
4. Important Points to note
they ask for aggregate marks.
I don't think you will have any problem.