Click on the check box next to the Invoice that you wish to apply a payment to.
A popup with a Apply Payment Button will appear and you can click on the Apply Payment button
You will be taken to the Payment screen where you will see the Invoice listed along with a Payment amount field.
The full amount owing will automatically populate the Payment Amount field.
If you the amount that you wish to apply against this Invoice is not the full amount then you can adjust this to the actual amount paid. Otherwise leave it the full amount owning and this will be applied to the Invoice.
Save this Payment by clicking on the Save button. You will be taken back to the Who Owes me screen.