When applying payments in QuickBooks, both new payments and credit memos can be applied to multiple invoices at the same time.  When this occurs, QuickBooks does not specifically track which credit memo paid which specific invoice.  This means that in Crik-IT we can not indicate specifically which invoice was paid by a particular credit memo.  Here's an example.

Payment & credits being applied to multiple invoices in QuickBooks:

A check (Chk 123412) AND part of a credit memo are being used together to partially pay 5 different invoices.

Here's the information QuickBooks provides to Crik-IT about this payment "session".  Note that there is no indication about which invoice(s) were paid by the check and which were paid by the credit memo.

The info QuickBooks gives us shows that 5 invoices had payments applied during this session, for a total of $50 paid on those invoices.  We can see that $25 was used from a credit memo (CM-10037) in this payment, but QuickBooks doesn't tell us specifically WHICH invoices were paid by the credit memo and which invoices were paid by the check.  The payment reference number is shown even on the credit memo info QuickBooks sends to Crik-IT, so we know that $25 of that credit memo was applied when the Chk 123412 payment was being applied.  It appears that QuickBooks does not track the specifics.