JOSAA has come up with new rules and regulations and this has made the payment of partial admission fee that is (Rs.40,000 for GEN, GEN-EWS, OBC-NCL and Rs 20,000 for SC, ST, PwD Candidates ).
You have to pay this fee in order to retain the seat that is allotted to you in rounds 1-6 of JOSAA counseling.
You can read an answer related to the fees of IIT's/NIT's here: - Does one have to pay anything if he gets admission in any NIT/IIT under JKPMSSS? And does he get money other than college fee? - pmsss.in
You can pay this Partial admission fee using Net Banking, Debit Card, Credit card, OR State Bank of India e-challan by logging in to your account on the JOSAA portal using your login credentials.
Hope this helped, feel free to ask if you have more doubts.