I have just paid 2 supplier invoices & tried to redeem a credit note against them but cannot seem to reconcile the credit

Hi accounts393, 

Thanks for joining us here on the Community. Can I check which screen you're viewing to reconcile this? 

Credits don't post to a payment account and so you won't see these on the main 'Reconcile' screen when reconciling a bank.

To apply the credit to the supplier invoices, select 'make payment' on one bill, on the following screen under 'Outstanding Transactions' tick both bills and then scroll to 'Credits' and tick the supplier credit - the total bill payment should then show as 0.00.