You can match these manually through the Purchase Enquiry:
From the Accounts Desktop select the Enquiries tab.
Select Supplier Enquiry.
Put in the Supplier Reference you require.
Select Search.
Either double click or select View.
Go to Transactions tab.
Select the receipt/payment by highlighting the correct one and select Match.
The box will come up with all your invoices/credit notes that are not paid and you can select one to allocate the monies against.
You can select old invoices if you have a positive and negative allocation to do that contra each other off but do the receipt/payment first.
This is through the radio button at the top 'show all invoices'.
Select Apply.
Select OK, then go and do the next allocation against either the same invoice or a different one if required.