Hello Manoj 

For all India quota counseling the refundable amount is RS 1000 for Ur category which needs to be filled online.Abd you will be able to pay for it only after you upload all the documents correctly along with your photograph and signature.

Once do all that then payment can be done through net banking , credit or debit card.And choice filling will be possible after payment is done

If you aren't allowed to pay there is some problem in some step or procedure .

Also I am sharing with you the link below which will help you understand the procedure better , please go through it .If you have any doubts please feel free to contact.

https://medicine.careers360.com/articles/how-fill-neet-application-form 

All the best