Once Round 6 of Counselling Process is over, IIT Roorkee will personally mail each and every new admit with further instructions regarding Mode of Fee Payment and Registration. Most probably this year their will be Online Registration, Induction and Verification Process besides as usual the Fee Payment by NET Banking, Debit Card or E-Challan at nearest Bank Branch. Keep patient and wait for Round 6 to end.

Secondly as far as deduction in fee is considered, I believe unless you are SC/ST you will have to pay the full fees now, however it will be adjusted next semester onwards through your respective merit cum mean/scholarship scheme.