If you have a customer that is also a supplier and you have a case when you need to collect from the customer on an invoice and you also need to pay the supplier(same as the customer) for a bill, follow the steps below.
Go to Setup menu, Entity settings, Payment Receipts, check the checkbox for Show All GL Accounts For Payment Receipt . Save the new setting.
If the customer owes you money after the invoice and bill is settled, you would first record a payment on the invoice owed with the amount you owe on the bill. Choose the supplier prepayment account for this supplier under Receive to Account. Enter the amount on the bill as the payment amount. Post the payment receipt. This will reduce the amounts owing on the invoice by the amount on the bill.
Record another payment against the customer for the net amount the customer owes you.
Next step is to clear payment for the bill to the supplier. Go to Bills menu, make payment, choose Apply prepayment option under Pay from account. Then choose the supplier from list. Choose the bills you are paying. Make sure the bill payment matches the balance on the supplier prepayment account. Post the bill payment and this bill will be considered paid in the system