When a client pays, do I have to mark the invoice as paid myself?

No. Each payment auto-reconciles the invoice — when money comes in, Kliently matches it to the invoice and updates the status for you. The invoice moves to paid, and its smart reminders stop, without any manual step on your end.

That keeps your books honest in real time: what shows as outstanding is genuinely outstanding, and what shows as paid genuinely cleared. For manual bank transfers, where there's no automatic signal, you confirm receipt and the same reconciliation follows.