Fristly, I couldn't understand when you are not interested in the particular branch then why you have filled that.

May be you were too excited for that college.

Regarding, your query, it is specifically mentioned in the JAC counseling rules, student have to fill the JAC fees as soon he gets enrollled in any of the course he/she listed

So, Yes you have to pay the required fees, else you would be kick out from the subsequent rounds.

Thank You