Here's how to record a payment from the business to a user, reimbursing expenses that the user has paid for personally, or mileage that he or she has travelled in his or her own car.
Once you've entered the expenses and mileage into FreeAgent, you can check how much that user is owed by going to Expenses and choosing that user from the left-hand menu.

Make sure that you've got an up-to-date view selected, for example 10 Most Recent, and check the running balance. Remember that you won't see the running balance if you choose the "All" view.

Once you know how much to pay the user, do so.
Then we come to recording that payment on FreeAgent.
Upload your transactions, or enter them manually. But whichever method you choose, the payment type needs to be 'Money Paid to User'.

Make sure you're paying from a bank account that's ticked as a business account. You can't pay users from a personal bank account.
Choose the correct user from the list.

For the reason for the payment, choose 'Expense Payment'.

Once you've finished entering the payment, select 'Create and Finish' or 'Create and Add Another' if you've put this transaction in manually, or 'Create New Explanation' if you've uploaded it. Or select 'Cancel' if you want to start again.
Back under Expenses, you can see that the payment to this user is showing on the screen and the running balance amount this user is owed has gone down.

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