This article explains what to do when you receive a single payment from a customer that pays off more than one invoice.
Navigate to the bank transaction that shows the full amount that your customer paid you.
From the ‘Invoice’ drop-down, select the first invoice to be split out from the transaction.
Select ‘Explain Transaction’
FreeAgent will then create a transaction on a new line for the amount of that invoice. You can repeat this process until all the invoices for that payment have been split out.
It's fine to have multiple entries explaining a single transaction like this - the only important thing is that the transaction is fully explained.