Hi Amit Kumar.

In the counselling of WBJEE, if you're alloted a seat, you have to pay the fee and and physically report at the reporting centre with the documents. From there, you can either confirm that seat or choose for upgradation. If chosen for upgradation and you get a higher choice in the next round, you have to report at the reporting centre, and there is no need to pay another fee of 5000. You only have to pay it once, when you get the seat for the first time. You can see the steps and all details regarding WBJEE counselling in this article.

https://engineering.careers360.com/articles/wbjee-counselling

Good Luck.