Scenario:

Customer rent a booth from you for RM1000. When they directly bank in to your account, the bank charges RM0.50. Hence your bank will show RM999.50

To solve the following

Please go to Finance --> Receipt Voucher

Tie to GL : Expenses : RM1000

Then you wait for your bank statement to come.
Normally there's one part, you will be able to see the total lumpsum bank charges.

Go to Finance --> Create Payment Voucher --> place lump sum figure

Tie to GL : Interest bank charges : RM x

This way, when you do your bank recon also will be easier.