Here's how to record a receipt from your customer that pays off just one invoice. (You can also mark more than one invoice as paid with one payment.)
Option 1: If you're uploading bank transactions
If you're uploading your bank transactions, you'll see the receipt coming in as one of your unexplained transactions.
Select the receipt.
Then explain it with type Invoice Receipt. FreeAgent will guess which invoice this relates to. If it's guessed right, you can just save the explanation. If it's guessed wrong, remove the guess by selecting the cross at the right of the 'Invoice' box, and type in a reference or amount for FreeAgent to search for the correct one.
When you're sure you have chosen the right invoice for this receipt, save the explanation.
Option 2: Add a Manual Payment button
When you've marked an invoice as sent, you'll see it has a button at the top saying "Add a Manual Payment".
If the money was paid into the bank account selected to display remittance advice on this invoice, you can use this button to mark the invoice as paid. If the money was paid into a different account (for example, your business's savings account, or your cash account), don't use this button.
To use the Add a Manual Payment option, just select the button.
Fill in the details on this screen, including when the invoice was paid.
Save that entry.
You can use this option even if you're explaining uploaded transactions. When you explain this receipt, you'll see an extra box asking if you want to use an existing manual entry. Select the Use Selected Entry button.
Option 3: Manual bank entry
If you're not uploading your bank transactions for the bank account which this receipt arrived in, and that bank account isn't your primary bank account, then you'll need to enter a manual invoice receipt.
Use type Invoice Receipt. In the 'Invoice' box, type in the invoice reference number, contact name, or total amount, to help FreeAgent search for the right invoice to allocate to this receipt. When it's found the right one, select that invoice to select it.
Save the entry.