Hi KirstenBl
I'm sorry to see that no one has replied to you yet. If I understand your post correctly you've applied full payment to an order which has then been converted to two invoices. If that's correct the steps would be:
1. order with payment applied
2. convert the order to an invoice with some items on Backorder, invoice now has a credit amount in Balance due:
3. a new order is created for the backordered items with an amount owing, convert that order to an invoice:
So you've got one invoice with a credit balance and one with an amount owing. Go to Sales Register>>Returns & Credits tab>>click on the credit invoice and Apply to sale. Record the transaction:
Both invoices are closed.
Before applying the credit to the second invoice the customer wouldn't have a statement because of the credit amount on the first invoice so they don't actually owe anything. The second invoice would show as outstanding because the credit hadn't been applied so the invoice was still open and unpaid.
Please let me know if I've misunderstood or you need further help.
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