First head to the Banking tab, and select the relevant account and transaction. When you've found the right transaction, hit 'More Options' to fully expand it. Next, explain the payment as type Bill Payment. Please note, if you have no outstanding bills then you won't be able to see Bill Payment as an option in the Type list.
Then search by reference, amount or contact to help FreeAgent find the bill you're paying. Choose the correct bill from the list when it appears. Finally, select 'Create New Explanation'.
If you're not uploading your bank statements, you can enter the payment manually.
Firstly, find the bill on the list on the Bills screen, then select it by clicking on the Bill reference.
Enter a payment against this bill by selecting the Pay Bill button.
This will bring up a screen where you can enter a manual payment to pay this bill from your primary bank account, with the compulsory fields filled in for you. When you're done, click 'Create and Finish'.
When should I not use the Pay Bill button?
If you have paid this bill from an account other than your primary bank account, don't use the Pay Bill button.
If you're uploading your bank statements, you can still use this button to enter the payment. When you come to do the upload and explain the transaction, so long as the transaction has the correct date and value, FreeAgent will give you the option to "Use Existing Manual Entry" when you explain it, and avoid putting it in twice.
The alternative way to manually enter a payment is by going to the Banking screen and selecting the bank account from which you're paying this bill, then choosing More, and Add Transaction.
Choose type Bill Payment from the list, and enter the date and the amount of the payment, as well as who you're paying.
Remember, if you have no outstanding bills then you won't be able to see Bill Payment as an option in the Type list. Save the payment by selecting Create and Finish once you have recorded it.
That's how to enter payment that you've made to a supplier against a bill that you've already put on to FreeAgent. You can also make entries to pay off more than one bill at once.