Dear Mr. Mohan,
EPF online submission has been implemented since March and paid in April 2012 by the Indian government. All are compulsorily required to submit the contribution online only. I find it surprising how your regional office is accepting this.
Anyway, there is software for EPF that you can download from the EPFO website (a demo file has been attached for your reference). You need to enter the required employee master details, and then every month, you must enter the employee wages and LOP details. The system will automatically generate the challan that you can directly upload online. When entering the employee master and wages in the software, there is no need to fill up individually; you can directly upload the information in the software through an Excel file in the .CSV format.
For payments, you can pay through net banking.
Regards,
Sintralla