On the first payment (assuming it is more than the 1st invoice as you describe):

Select 1st and 2nd invoices. GnuCash will 'close out' the first one entirely, and apply the rest as a partial payment to invoice #2.

Otherwise, GnuCash doesn't know *which* subsequent invoices should have the payment applied. (and why you see that remainder as a credit or pre-payment on subsequent uses of the 'Process Payment' dialog)

If you do not select an invoice, you will always get it assigned as 'pre-payment' and the window offers a warning at the bottom that it will not be linked to any document.

Yes, you can always apply the pre-payments by selecting them with appropriate invoices. (that's how you accomplish such a task) But as you noted, how that shows up in the register and on reports will differ from how it would appear if you used the above procedure. (as it should in such a case)

On the 2nd Payment, select the 2nd invoice that still has a balance, and then the 3rd invoice. Again, if there is left-over payment, it will be retained as a pre-payment. If it is not sufficient to cover invoice #3, then that invoice will remain as pending for the amount remaining. If it perfectly pays off invoice #2 & #3, then they will both be fully closed out as paid.

Regards,
Adrien

On 12/16/20 5:21 PM, Garry Cooke wrote:
Hi, Customer has 3 invoices. Pays with 2 deposits into bank. On the imported 
bank transactions i select ‘process payment’. Select invoice, expecting amount 
to be applied to invoice and balance to applied to next invoice. Instead i get 
a credit to the customer. 2nd payment i leave invoice blank and get same 
result. I end up with 3 unpaid invoices and 2credits against customer. I 
attempted to resolve by selecting invoice and using to credit to pay, which 
worked. But when i print customer report to use as statement it has 3 
transactions included with $0. What am i missing? Why were the amounts not 
applied to the invoices when applied from incoming bank transaction?

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