Hi,
When we post incoming / outgoing flows with customer, then teh system creates an Accounts Receivable / Accounts Payable entry which gets reflected in the Balance Sheet. And then the payment / receipt is done by debiting / crediting the bank accounts, which can also be done through the automatic payment program.
On the other hand, when you post to a bank clearing account directly the bank inflow / outflow account gets hit immediately.
It is advisable to follow the first process as it cleary shows when the payment to the customer / vendor was actually done.
Warm regards,
Akhil Poddar