HI Pasan,
Yes is the short answer. The Payment Method you create is attached to a Payment format.
if you want to generate a file to pass into the banking network to do the bank transactions then you would attach to a method that outputs a file (if this is US based then its more common got ACH to be used in a business environment). you need to make sure you chose one that supports the currency or is using a %
If you are doing the banking separately (Keying in the transactions in your online banking site as an example) then you can attach to the EMPTY format for complete flexibility
Regards
John