If I apply for multiple branches in same IIT should I pay money every time during gate councelling

In COAP, you'll be given an offer. You can choose ONLY ONE offer in a round. You can choose 3 options - Accept and Freeze, Retain and wait & Reject and wait, for the offer. In the case of 1st and 2nd option, you have to visit the website of the concerned IIT and complete the procedures. For the 3rd one, you have wait for the next round.

So, if you accept an offer, you have to pay the fee. This can be the same in the case of Retain and wait. But, if you withdraw an offer after accepting it, you can get the money refunded.

I suggest you visit the official website of COAP for more details. And, you can also call them to rectify your doubts in the number provided.

http://coap.iitm.ac.in/#

Good luck.