If you want to register a supplier invoice as paid manually, go to Supplier Invoices - Supplier Invoice. Select the invoice you want to register as paid from the list:
Now you will see the invoice details. Click on Register Payment:
In the modal that appears you can change the payment date, payment method, paid amount and fill in any deviations. Deviations are e.g. reminder charges. Select the correct account in the Add Deviation Account field, click enter to get a new row if necessary.
When all the information is correct, click on Register Payment. Now your payment is registered as paid.