Service tax payment against bills

Hi All,

As per the latest amendments, When we raise Service Tax Bill to Client, within 30 days we have to pay challans to the Govt. But, One of our Client on which we had raised Bill on 02.09.2011 for2,50,000.00 failed to clear the dues till 01.10.2011 though we had paid the Service Tax Challan totaling25,750.00 before 30.09.2011 well within 30 days from the date of raising the Bill. And correspendingly filed our Quartely Service Tax Return.

Now, on 24.10.2011, the Client has certified the Bill but with deductions, now the Bill which was of2,50,000 now valued at2,07,000 and the Service Tax applicable will be 21,321.00. As a result the service tax challan paid is in excess by4,429.00 (25,750 - 21,321).

My Queries are:

1)   How can I avoid such a situation of excess payment of Service Tax Challan in the future. Should I raise performa  invoice and than Final Invoice with Service Tax.

2)   How can I adjust the excess service tax4,429.00 as the return filed was as per the Bill originally issued for2,50,000.00.

Thanks in advance