To add a Payment to an individual invoice record, select the invoice record from the Invoice section (i.e. left hand pane of the Invoice Payment screen). Then click the Add Payment button in the top left corner of the Payment Detail section. This will open the Payment window:
Here you can define the date the payment was received along with the amount you wish to add, and record any extra details in the Notes field. Once you have done that, click Add. The amount will appear below, highlighted in orange. If you wish to remove it, simply click Remove. You can add as many Payments as you wish. Once you are satisfied, click Save and the Payment you have recorded will be captured against the overall payment received in relation to this individual invoice.