We have recently migrated to Zoho and are transferring all our information.

Our company usually issues a retainer invoice, then allocates the payment to the retainer. We then issue the invoice, apply the retainer amount to the final invoice and then allocate the final payment.

However, we have received a payment for both the retainer and the final invoice in one. When trying to match this in the banking, it ends up as a credit because I cannot apply the retainer to the invoice before matching the final invoice payment. 

Please advise what the correct way or best practice method is in this case.