If you have one invoice but part of the invoice is Vatable and part is VAT exempt then you will need to:
Post two separate transactions to the system.
In general postings post either two PIO's or two PIN's one for the Vatable element and one for the VAT exempt element.
You can use the same invoice number on both and just accept the warning that you are using the same invoice number.
You can pay the full amount of the invoice in one payment either PPO or PPN for the full amount selecting both invoices.