Follow these steps to manually mark an invoice as paid:
Locate the invoice on the "Invoicing" page inside of your project. It should be listed under the "Open" or "Upcoming" tabs.
Click the "..." on the right side of the invoice item.
Select "Mark as Paid" and a popup will appear.
Confirm that the amount the client has paid you is correct. (If the client paid you a different amount than what was requested in the invoice, you can manually adjust the amount to the correct number.)
Select what method the client used to pay you. (Choose from options like Cash, Check, Bank/Wire Transfer, External Payment or Other)
Click "Confirm".
After completing these steps, you should see your invoice move to the "Paid" tab! You'll also see this update reflected on your Financial reports page.