Hi Sekar,
For APP configuration please follow the steps given in below link.
For cheque payment you need to configure in the system with help of ABAPER who will develop the form for cheque printing and this cheque printing form has to be assigned in your APP configuration.
Payment can be done by DMEE file as well.In DMEE SAP system creates the file(in .txt or .csv format) of vendors to be paid as the case may be and this file is then forwarded to bank for payment.
For DMEE configuration please follow the steps given in below link.
DMEE Configuration:Step By Step Part 1
For EBS configuration please follow the steps given in below link.
For EBS there are few prerequisite like you should ask for the file format from the bank.....Like MT940,MT942 etc.
Hope this will help you to understand the process and configuration steps.
Regards
Eugene