You have to pay  KEA fees of 45000 every year plus you will have to pay your college fees also every year. But the college fees may vary and may not be the same 35,840 for the second year. College fees might be slightly less for the second year .

First year you need to pay directly favoring KEA through challan or online payment(if applicable). Then report to college taking an admission order and there just pay prescribed college fee and hostel fee(if applicable)

Rest three years you need to pay both KEA fee and college fee in your college only.

Hope this helps