Dear Sudheer, First you have to register in any one of the three channels- KVPY, SCB and JEE.Kishore Vaigyanik Protsahan Yojana (KVPY) – Candidates will be offered admission on the basis of valid KVPY fellowship. The State or Central Board Channel(SCB) students will have to appear in aptitude test. Joint Entrance Examination of Indian Institutes of Technology (JEE) channel – Candidates with valid JEE Advanced 2019 scores are eligible for direct admission.

So when the admission portal opens it will ask you to choose your channel ,if you choose KVPY channel then at the time of counceling your KVPY marks will be considered for admission.The counceling start between june and july.

For further more details on admission procedure check the link below:

link: "https://engineering.careers360.com/articles/iiser-admission"

link for official site:https://www.iiseradmission.in/?page_id=15

Hope i was able to solve your doubt,Thank you!