The situation is that another company made a payment for freight cost on behalf of my company. I would like to know how to record in a journal entry.

@lleawe0705-aspen 

There's no need to use a journal entry.  First, create a bank account in QB called 'Clearing Account'.  Then, pay the bill for the freight cost using the Clearing Account as the payment account.  Receive payment on the customer's invoice for the same amount and deposit it into the Clearing Account.  The bill is now paid, the customer's open invoice has a payment applied for the same amount.  Make notes on both the bill and invoice to connect the two.