Dear Rahul 

In case you get a seat in NIT under CCMN counselling and at the same time get a seat in the third and final list of IIT JAM admissions, then you can simply surrender the seat you get in NIT and get the refund and accept your desired seat in IIT JAM. 

Note that there will be dates stipulated for surrendering, during which you will have to make a choice to either accept or surrender a seat. You will get complete refund after deduction of INR 1000/- as processing fee. 

Now, in a reverse case scenario, wherein you get a seat in IIT third and final list and pay the seat booking amount, and then recieve a seat in NIT and wish to take that up, in that case, you will not be liable to get refund of the seat booking amount from IIT, since no refund is permissible after seat booking amount is paid after third and final list of IIT. The seat booking amount at IIT JAM is 10,000/-. 

Hope it answers you. 

All the best!