When you explain a bank transaction, you can alter the explanation amount (which by default is set to the full amount of the transaction).
This is how to deal with the situation when you receive one payment from a customer that pays off more than one invoice.
The transaction will intially show the full amount that the customer paid you in the "Credit Value" box:

You need to change the amount in the "Credit Value" box to match the amount of the first invoice:

FreeAgent will then create a new transaction for the remainder of the receipt, which you can explain against the rest of the invoice(s) that the customer paid you for.
You can even mix debit and credit explanations against a single transaction (for example a mixture of invoices and credit notes) in the same way.
It's fine to have multiple entries explaining a single transaction like this - the only important thing is that the transaction is fully explained.
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