Hi Himanshu, 

it would have been better if you could please specify for which entrance exam application are you talking about? Because different exam applications demand different criteria. However  as for neet ug as far as i remember the total marks written in your marksheet of your board exams is to be taken in account for calculating your percentage  You will to see the instructions once you start filling up your application form. Also i feel it will be wiser of you to ask your friends also who have already filled up the application form.

hope this helped. All the best for your upcoming exams. :)