There are two different ways you can mark a PACE invoice as paid (this will depend on whether your organisation has our reconciliation feature enabled or not)

Please note you can include your PACE and non-PACE invoices in the same mark as paid process
1. If you don't use reconciliation you will be able to select the PACE invoice via the invoice entry screen (filtering via the Extracted status)
2. You would then use the invoices listed
3. Once selected use the Action button and click Mark Invoices as Paid
4. If you have reconciliation turned on you will follow the standard reconciliation process.