If say you had an amount pre paid by a customer of £6000. You post as a PA (creditors a/c) a month or so later, you raise the invoice but for only part of that amount £5500 - why cant you allocate this to the PA leaving the £500 o/s?? You can easily do this on other accounting software.
You can - Use 'Apply Credit' after you generate the invoice
The payment on account will appear as a credit