Hi anjali, 

According to nert entrance exam rules you should passed your 12th (inter)  examination with 50% aggregate marks in four subject that is biology, physics, chemistry and one more other subject. 

So if you have scored 50% then you are eligible to give neet entrance exam. So you should enter the marks which you have got in your 12th class certificate. 

Your certificate will also be checked at the time of document verification so enter the marks you had got in your certificate and it does not matter out of how much you got marks. Only thing matter is that you should score 50% or more. 

For any other information you can ask us.