How to receive balance of electronic credit ledger - gta service

WE ARE RUNNING GTA SERVICE FOR WHICH WE ARE GIVING TWO SERVICES.

1.TRANSPORTATION AND

2.CLEARING CHARGES.

FOR TRANSPORTATION GST IS NOT CHARGING IN INVOICE AND THE SAME WAS PAID BY PARTY. 

AND FOR CLEARING WE ARE CHARGING GST ON BILL AND THE SAME WAS COLLECTED AND PAID BY US.

MY DOUBT IS WHETHER WE CAN CLAIM INPUT ON EXPENSES.

FYI WE HAD SHOWN INPUT IN 3B AND THE SAME WAS ACCUMULATED IN HUGE AMOUNT. PLEASE ADVICE HOW TO GET REFUND OF BALANCES IN ELECTRONIC CREDIT LEDGER.