How do I record a payment that did not come through the pay link?

Mark paid is the close-out for money that arrived outside DeskOps — a check in the mail, cash on the job, a bank transfer you took directly. It records the payment against the invoice so the balance, the Money page and your tax position all move together. A partial amount leaves the invoice part-paid with the remainder still owed. If Mark paid was a mistake, the invoice detail has an undo for it — except for a payment dated in a month you have closed, which stays as it is. If that payment had left the invoice overpaid and the extra was kept as the customer's account credit, the undo takes the unused credit back too; if the customer has already used it, the undo says so and nothing changes. If the customer really paid you, leave it alone. A payment that belongs to an invoice is taken back from the invoice, never deleted from the Money page on its own, so the invoice and your revenue can never disagree.