When you record a payment that does not match the balance, the screen asks what happened to the difference. The answer decides which account absorbs it, and the three are not interchangeable.
·Leave it owing — the rest is still coming. This is the default, because the commonest short payment is a first instalment.
·The bank took it in transit — the customer paid in full and the wire cost two dollars. It books as a bank fee.
·You agreed to it — books as a discount given.
·You are giving up on it — books as bad debt.
Why the reason matters
Filing a bank fee as a discount says the customer paid less than they owed, which is a different sentence about a different person. The two land in different places on your profit and loss, and afterwards nobody can tell them apart.