You can create a zero entry posting to pick up the invoice and the payment so either a PPO or PPN:
From the Main Menu go to General Postings.
Select PPO/PPN and click NEW.
Put the correct Nominal/Matter in and then select the Grid for the allocations of the invoices.
Select the Payment and Invoice from the list and make sure the payment amount comes back at zero.
Select the Floppy disk button.
After all of the postings are done that are required you can select POST.