You are supposed to pay the whole fee. In Inda marks don't matter for Fee waiver, your caste matters so if you are SC/ST then congo!!
else yes, you need to pay whole fees!!

During admission, you pay some fee online. That gets deducted from your total fee which you pay later when college reopens

Yes when YOU get a sit in IIT /NIT then you have to pay some sit booking amount approximately 5-10k is enough to pay that time this advance amount will be manage with your total fee
Hope it help you.

Hello Aditi,
It's great to hear from you that you already have seen the dream to take admission in IIT or NIT. Dreaming big is the first step to achieve  anything you want. So very first of all congratulations for taking a step towards your better future.
So regarding your question, yes you will have to pay fees in IIT or NIT avichal institution you take admission in yes you will have to pay fees in IIT or NIT or whichever institution you take admission in. And very first of all you will have not have to pay fees as much it is in private institution for engineering as most of the expenses of students are taken by government of India for the better future of Indian students in Indian economy. You'll have to pay minimalistic fees for quality education that you will be getting in those institutions. 
But at the same time you'll also be able to apply for many of the scholarships available so it will not be a big load for you.
Hope I answered your query. Thank you so much for reading and best of luck for your future.

Dear Aditi,

Yes, you need to pay the fees there are some exemptions as well you can check below

- The SC/ST/Differently abled students shall get complete fee waiver

- The most economically backward students (whose family income is less than Rs.1 lakh per annum) shall get full remission of the fee. 

- The other economically backward students (whose family income is between Rs.1 lakh to Rs.5 lakh per annum) shall get remission of 2/3rd of the fee.

 

Good luck!!