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Where invoices come from

An invoice is generated from the quote, not the job. That is deliberate: what you bill should match what the customer accepted, not what production happened to do. One quote can carry several invoices — a deposit and a balance, or staged billing on a long run.

Sending and settling

Send the invoice by email and the customer gets a PDF link. When payment lands, mark it paid. If something goes wrong you can unmark it, void it, or record a refund — all of which stay on the record rather than quietly changing history. If a customer claims they have paid and they have not, dismissing the claim clears the flag.
Marking money as received is a separate permission from creating invoices. In the API it is the invoices.settle scope. An integration that raises invoices does not automatically get to say they were paid.

Pushing to accounting

With Xero or QuickBooks connected, push an invoice straight into your accounts rather than re-keying it. The push is its own permission again (invoices.sync), because it writes into a system outside PRINTOOLS. See Apps and automation.

PDFs

Quote and invoice PDFs are available as links that expire after fifteen minutes. Generate one when you need it rather than storing the URL — a stale link will not open.