You can clear incoming and outgoing payments directly when posting via the entry screen.

Select Accounting > Posting > Batch posting or Dialogue posting to clear the invoices directly when entering the payments.

Enter a payment here:

Click the Add button (CTRL+E key combination) in the clearing area and select the voucher(s) against which you want to post using the selection list. Here you have the option of splitting postings. As soon as you click on Post, the relevant items disappear from the open items list or, depending on the setting, are marked as cleared with a green tick.

The Clearing section is only displayed if a person account has been addressed.