I am in a bit of a quandary as to how I should handle a remittance that has negative entries.

To give a bit of a background... Once we receive money from a firm, I post the payment to a G/L account - "Waiting for Remittances". Upon receiving the remittance, I then debit the G/L account and start allocating the payments to the company and linking the invoices. Now in this case, the company has paid an amount into our account and I have started allocating the payment according to the remittance and linking the invoices to the payments. The problem is though, the company has reversed some of the payments from a previous remittance. So I duly debited the company with these reversals. The only problem here is that the reversed payment does not link to the invoice. So when I draw out a statement it still looks as if those invoices have been paid and that there is one large amount showing as the payment reversal. What is the correct way to do these payment reversals?